diff --git a/_sources/af1/af1.4.ipynb b/_sources/af1/af1.4.ipynb
new file mode 100644
index 0000000..9cbf6c2
--- /dev/null
+++ b/_sources/af1/af1.4.ipynb
@@ -0,0 +1,715 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "id": "LBNBl2exUYWu"
+   },
+   "source": [
+    "# Af1.4\n",
+    "\n",
+    "The **[Af1.4](af1.4):  _Anopheles gambiae_ data resource** contains single nucleotide polymorphism (SNP) calls and SNP haplotypes from whole-genome sequencing of 733 mosquitoes.\n",
+    "\n",
+    "More information about this release can be found in the [data resource website](https://www.malariagen.net/data_package/af14-anopheles-funestus-data-resource/).  \n",
+    "\n",
+    "This page provides an introduction to open data resources released as part of `Af1.4`. \n",
+    "\n",
+    "If you have any questions about this guide or how to use the data, please [start a new discussion](https://github.com/malariagen/vector-public-data/discussions/new) on the malariagen/vector-open-data repo on GitHub. If you find any bugs, please [raise an issue](https://github.com/malariagen/vector-public-data/issues/new/choose)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "id": "kJqs4cXppk8j"
+   },
+   "source": [
+    "## Terms of use\n",
+    "\n",
+    "Data from this project will be made publicly available before journal publication. Unless otherwise stated, analyses of project data are ongoing and publications are in preparation by project partners, and it is not permitted to use project data for publication (including any type of communication with the general public) without prior permission from the originating partner studies. \n",
+    "\n",
+    "Although malaria is generally an endemic rather than an epidemic disease, and the focus of this project is on surveillance of disease vectors rather than pathogens, our data terms of use build on MalariaGEN's approach to data sharing, and adopt norms which have been established for rapid sharing of pathogen genomic data during disease outbreaks. The primary rationale for this approach is that malaria remains a public health emergency, where ethically appropriate and rapid sharing of genomic surveillance data can help to detect and respond to biological threats such as new forms of insecticide resistance, and to adapt malaria vector control strategies to different settings and changing circumstances.\n",
+    "\n",
+    "The publication embargo for all data on this release will expire on the **16th of August 2026**. \n",
+    "\n",
+    "If you have any questions about the terms of use, please email [support@malariagen.net](mailto:support@malariagen.net)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "id": "iNSicUCtpk8j"
+   },
+   "source": [
+    "## Partner studies\n",
+    "\n",
+    "- [1188-VO-SN-NIANG](https://www.malariagen.net/network/where-we-work/1188-VO-SN-NIANG) - _Anopheles gambiae_ vector surveillance in Senegal.\n",
+    "\n",
+    "- [1330-VO-GN-LAMA](https://www.malariagen.net/network/where-we-work/1330-VO-GN-LAMA) - _Anopheles gambiae_ vector surveillance in Guinea.\n",
+    "\n",
+    "- [1354-VO-KE-DONNELLY](https://www.malariagen.net/network/where-we-work/1354-VO-KE-DONNELLY) - _Anopheles_ vector surveillance in Kenya."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "id": "5RHbe7N6pk8k"
+   },
+   "source": [
+    "## Whole-genome sequencing and variant calling\n",
+    "\n",
+    "All samples in `Af1.4` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "id": "9Hfchko2pk8l"
+   },
+   "source": [
+    "## Data hosting\n",
+    "\n",
+    "Data from `Af1.4` are hosted by several different services. \n",
+    "\n",
+    "The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as [MyBinder](https://gke.mybinder.org/) and [Google Colab](https://colab.research.google.com/). Further information about analysing these data in the cloud is provided in the [cloud data access guide](cloud)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "id": "lTJ_EnvOpk8l"
+   },
+   "source": [
+    "## Sample sets\n",
+    "\n",
+    "The samples included in `Af1.4` have been organised into 1 sample set. \n",
+    "\n",
+    "Each sample set corresponds to a set of mosquito specimens from a contributing study. Study details can be found in the partner studies webpages listed above."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "id": "hGA4d7Yrpk8m",
+    "outputId": "c29827c1-0361-4926-c227-8f6e76c2a497",
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "%pip install -qq malariagen_data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Note:** To access the `Af1.4` release, you need to use the `pre=True` flag. \n",
+    "\n",
+    "This flag is used when more data will be added to this release, for the case of `Af1.4`, CNV data for the sample sets on this release will be included at a future date."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "id": "AnmzLmEgpk8n",
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [
+    {
+     "data": {
+      "application/javascript": [
+       "'use strict';\n",
+       "(function(root) {\n",
+       "  function now() {\n",
+       "    return new Date();\n",
+       "  }\n",
+       "\n",
+       "  const force = true;\n",
+       "\n",
+       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
+       "    root._bokeh_onload_callbacks = [];\n",
+       "    root._bokeh_is_loading = undefined;\n",
+       "  }\n",
+       "\n",
+       "const JS_MIME_TYPE = 'application/javascript';\n",
+       "  const HTML_MIME_TYPE = 'text/html';\n",
+       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
+       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
+       "\n",
+       "  /**\n",
+       "   * Render data to the DOM node\n",
+       "   */\n",
+       "  function render(props, node) {\n",
+       "    const script = document.createElement(\"script\");\n",
+       "    node.appendChild(script);\n",
+       "  }\n",
+       "\n",
+       "  /**\n",
+       "   * Handle when an output is cleared or removed\n",
+       "   */\n",
+       "  function handleClearOutput(event, handle) {\n",
+       "    function drop(id) {\n",
+       "      const view = Bokeh.index.get_by_id(id)\n",
+       "      if (view != null) {\n",
+       "        view.model.document.clear()\n",
+       "        Bokeh.index.delete(view)\n",
+       "      }\n",
+       "    }\n",
+       "\n",
+       "    const cell = handle.cell;\n",
+       "\n",
+       "    const id = cell.output_area._bokeh_element_id;\n",
+       "    const server_id = cell.output_area._bokeh_server_id;\n",
+       "\n",
+       "    // Clean up Bokeh references\n",
+       "    if (id != null) {\n",
+       "      drop(id)\n",
+       "    }\n",
+       "\n",
+       "    if (server_id !== undefined) {\n",
+       "      // Clean up Bokeh references\n",
+       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
+       "      cell.notebook.kernel.execute(cmd_clean, {\n",
+       "        iopub: {\n",
+       "          output: function(msg) {\n",
+       "            const id = msg.content.text.trim()\n",
+       "            drop(id)\n",
+       "          }\n",
+       "        }\n",
+       "      });\n",
+       "      // Destroy server and session\n",
+       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
+       "      cell.notebook.kernel.execute(cmd_destroy);\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  /**\n",
+       "   * Handle when a new output is added\n",
+       "   */\n",
+       "  function handleAddOutput(event, handle) {\n",
+       "    const output_area = handle.output_area;\n",
+       "    const output = handle.output;\n",
+       "\n",
+       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
+       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
+       "      return\n",
+       "    }\n",
+       "\n",
+       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
+       "\n",
+       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
+       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
+       "      // store reference to embed id on output_area\n",
+       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
+       "    }\n",
+       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
+       "      const bk_div = document.createElement(\"div\");\n",
+       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
+       "      const script_attrs = bk_div.children[0].attributes;\n",
+       "      for (let i = 0; i < script_attrs.length; i++) {\n",
+       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
+       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
+       "      }\n",
+       "      // store reference to server id on output_area\n",
+       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  function register_renderer(events, OutputArea) {\n",
+       "\n",
+       "    function append_mime(data, metadata, element) {\n",
+       "      // create a DOM node to render to\n",
+       "      const toinsert = this.create_output_subarea(\n",
+       "        metadata,\n",
+       "        CLASS_NAME,\n",
+       "        EXEC_MIME_TYPE\n",
+       "      );\n",
+       "      this.keyboard_manager.register_events(toinsert);\n",
+       "      // Render to node\n",
+       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
+       "      render(props, toinsert[toinsert.length - 1]);\n",
+       "      element.append(toinsert);\n",
+       "      return toinsert\n",
+       "    }\n",
+       "\n",
+       "    /* Handle when an output is cleared or removed */\n",
+       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
+       "    events.on('delete.Cell', handleClearOutput);\n",
+       "\n",
+       "    /* Handle when a new output is added */\n",
+       "    events.on('output_added.OutputArea', handleAddOutput);\n",
+       "\n",
+       "    /**\n",
+       "     * Register the mime type and append_mime function with output_area\n",
+       "     */\n",
+       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
+       "      /* Is output safe? */\n",
+       "      safe: true,\n",
+       "      /* Index of renderer in `output_area.display_order` */\n",
+       "      index: 0\n",
+       "    });\n",
+       "  }\n",
+       "\n",
+       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
+       "  if (root.Jupyter !== undefined) {\n",
+       "    const events = require('base/js/events');\n",
+       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
+       "\n",
+       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
+       "      register_renderer(events, OutputArea);\n",
+       "    }\n",
+       "  }\n",
+       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
+       "    root._bokeh_timeout = Date.now() + 5000;\n",
+       "    root._bokeh_failed_load = false;\n",
+       "  }\n",
+       "\n",
+       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
+       "     \"<div style='background-color: #fdd'>\\n\"+\n",
+       "     \"<p>\\n\"+\n",
+       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
+       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
+       "     \"</p>\\n\"+\n",
+       "     \"<ul>\\n\"+\n",
+       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
+       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
+       "     \"</ul>\\n\"+\n",
+       "     \"<code>\\n\"+\n",
+       "     \"from bokeh.resources import INLINE\\n\"+\n",
+       "     \"output_notebook(resources=INLINE)\\n\"+\n",
+       "     \"</code>\\n\"+\n",
+       "     \"</div>\"}};\n",
+       "\n",
+       "  function display_loaded(error = null) {\n",
+       "    const el = document.getElementById(null);\n",
+       "    if (el != null) {\n",
+       "      const html = (() => {\n",
+       "        if (typeof root.Bokeh === \"undefined\") {\n",
+       "          if (error == null) {\n",
+       "            return \"BokehJS is loading ...\";\n",
+       "          } else {\n",
+       "            return \"BokehJS failed to load.\";\n",
+       "          }\n",
+       "        } else {\n",
+       "          const prefix = `BokehJS ${root.Bokeh.version}`;\n",
+       "          if (error == null) {\n",
+       "            return `${prefix} successfully loaded.`;\n",
+       "          } else {\n",
+       "            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n",
+       "          }\n",
+       "        }\n",
+       "      })();\n",
+       "      el.innerHTML = html;\n",
+       "\n",
+       "      if (error != null) {\n",
+       "        const wrapper = document.createElement(\"div\");\n",
+       "        wrapper.style.overflow = \"auto\";\n",
+       "        wrapper.style.height = \"5em\";\n",
+       "        wrapper.style.resize = \"vertical\";\n",
+       "        const content = document.createElement(\"div\");\n",
+       "        content.style.fontFamily = \"monospace\";\n",
+       "        content.style.whiteSpace = \"pre-wrap\";\n",
+       "        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n",
+       "        content.textContent = error.stack ?? error.toString();\n",
+       "        wrapper.append(content);\n",
+       "        el.append(wrapper);\n",
+       "      }\n",
+       "    } else if (Date.now() < root._bokeh_timeout) {\n",
+       "      setTimeout(() => display_loaded(error), 100);\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  function run_callbacks() {\n",
+       "    try {\n",
+       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
+       "        if (callback != null)\n",
+       "          callback();\n",
+       "      });\n",
+       "    } finally {\n",
+       "      delete root._bokeh_onload_callbacks\n",
+       "    }\n",
+       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
+       "  }\n",
+       "\n",
+       "  function load_libs(css_urls, js_urls, callback) {\n",
+       "    if (css_urls == null) css_urls = [];\n",
+       "    if (js_urls == null) js_urls = [];\n",
+       "\n",
+       "    root._bokeh_onload_callbacks.push(callback);\n",
+       "    if (root._bokeh_is_loading > 0) {\n",
+       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
+       "      return null;\n",
+       "    }\n",
+       "    if (js_urls == null || js_urls.length === 0) {\n",
+       "      run_callbacks();\n",
+       "      return null;\n",
+       "    }\n",
+       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
+       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
+       "\n",
+       "    function on_load() {\n",
+       "      root._bokeh_is_loading--;\n",
+       "      if (root._bokeh_is_loading === 0) {\n",
+       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
+       "        run_callbacks()\n",
+       "      }\n",
+       "    }\n",
+       "\n",
+       "    function on_error(url) {\n",
+       "      console.error(\"failed to load \" + url);\n",
+       "    }\n",
+       "\n",
+       "    for (let i = 0; i < css_urls.length; i++) {\n",
+       "      const url = css_urls[i];\n",
+       "      const element = document.createElement(\"link\");\n",
+       "      element.onload = on_load;\n",
+       "      element.onerror = on_error.bind(null, url);\n",
+       "      element.rel = \"stylesheet\";\n",
+       "      element.type = \"text/css\";\n",
+       "      element.href = url;\n",
+       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
+       "      document.body.appendChild(element);\n",
+       "    }\n",
+       "\n",
+       "    for (let i = 0; i < js_urls.length; i++) {\n",
+       "      const url = js_urls[i];\n",
+       "      const element = document.createElement('script');\n",
+       "      element.onload = on_load;\n",
+       "      element.onerror = on_error.bind(null, url);\n",
+       "      element.async = false;\n",
+       "      element.src = url;\n",
+       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
+       "      document.head.appendChild(element);\n",
+       "    }\n",
+       "  };\n",
+       "\n",
+       "  function inject_raw_css(css) {\n",
+       "    const element = document.createElement(\"style\");\n",
+       "    element.appendChild(document.createTextNode(css));\n",
+       "    document.body.appendChild(element);\n",
+       "  }\n",
+       "\n",
+       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.1.min.js\"];\n",
+       "  const css_urls = [];\n",
+       "\n",
+       "  const inline_js = [    function(Bokeh) {\n",
+       "      Bokeh.set_log_level(\"info\");\n",
+       "    },\n",
+       "function(Bokeh) {\n",
+       "    }\n",
+       "  ];\n",
+       "\n",
+       "  function run_inline_js() {\n",
+       "    if (root.Bokeh !== undefined || force === true) {\n",
+       "      try {\n",
+       "            for (let i = 0; i < inline_js.length; i++) {\n",
+       "      inline_js[i].call(root, root.Bokeh);\n",
+       "    }\n",
+       "\n",
+       "      } catch (error) {throw error;\n",
+       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
+       "      setTimeout(run_inline_js, 100);\n",
+       "    } else if (!root._bokeh_failed_load) {\n",
+       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
+       "      root._bokeh_failed_load = true;\n",
+       "    } else if (force !== true) {\n",
+       "      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
+       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  if (root._bokeh_is_loading === 0) {\n",
+       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
+       "    run_inline_js();\n",
+       "  } else {\n",
+       "    load_libs(css_urls, js_urls, function() {\n",
+       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
+       "      run_inline_js();\n",
+       "    });\n",
+       "  }\n",
+       "}(window));"
+      ],
+      "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded(error = null) {\n    const el = document.getElementById(null);\n    if (el != null) {\n      const html = (() => {\n        if (typeof root.Bokeh === \"undefined\") {\n          if (error == null) {\n            return \"BokehJS is loading ...\";\n          } else {\n            return \"BokehJS failed to load.\";\n          }\n        } else {\n          const prefix = `BokehJS ${root.Bokeh.version}`;\n          if (error == null) {\n            return `${prefix} successfully loaded.`;\n          } else {\n            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n          }\n        }\n      })();\n      el.innerHTML = html;\n\n      if (error != null) {\n        const wrapper = document.createElement(\"div\");\n        wrapper.style.overflow = \"auto\";\n        wrapper.style.height = \"5em\";\n        wrapper.style.resize = \"vertical\";\n        const content = document.createElement(\"div\");\n        content.style.fontFamily = \"monospace\";\n        content.style.whiteSpace = \"pre-wrap\";\n        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n        content.textContent = error.stack ?? error.toString();\n        wrapper.append(content);\n        el.append(wrapper);\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(() => display_loaded(error), 100);\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.1.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n      try {\n            for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n\n      } catch (error) {throw error;\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import malariagen_data\n",
+    "af1 = malariagen_data.Af1(pre=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/",
+     "height": 927
+    },
+    "id": "qsElasBepk8n",
+    "outputId": "4bf80a06-c2e8-4d2d-b4a6-99c8c66da7db",
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>sample_set</th>\n",
+       "      <th>sample_count</th>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>study_id</th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>1188-VO-SN-NIANG</th>\n",
+       "      <td>1188-VO-NIANG-NIEL-SN-2304-VMF00259</td>\n",
+       "      <td>71</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1330-VO-GN-LAMA</th>\n",
+       "      <td>1330-VO-GN-LAMA-VMF00250</td>\n",
+       "      <td>196</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1354-VO-KE-DONNELLY</th>\n",
+       "      <td>1354-VO-KE-DONNELLY-VMF00281</td>\n",
+       "      <td>466</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                                              sample_set  sample_count\n",
+       "study_id                                                              \n",
+       "1188-VO-SN-NIANG     1188-VO-NIANG-NIEL-SN-2304-VMF00259            71\n",
+       "1330-VO-GN-LAMA                 1330-VO-GN-LAMA-VMF00250           196\n",
+       "1354-VO-KE-DONNELLY         1354-VO-KE-DONNELLY-VMF00281           466"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df_sample_sets = af1.sample_sets(release=\"1.4\")\n",
+    "df_sample_sets[['study_id','sample_set', 'sample_count']].set_index('study_id')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "id": "yJ16OQ0Hpk8o"
+   },
+   "source": [
+    "Here is a more detailed breakdown of the samples contained within this sample set, summarised by country, year of collection, and species:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/",
+     "height": 1000
+    },
+    "id": "a1OMvuTxUWpJ",
+    "outputId": "9f872334-fd50-4649-990a-df60ea71c12c",
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "                                     \r"
+     ]
+    },
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th>taxon</th>\n",
+       "      <th>funestus</th>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>study_id</th>\n",
+       "      <th>sample_set</th>\n",
+       "      <th>country</th>\n",
+       "      <th>year</th>\n",
+       "      <th></th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th rowspan=\"3\" valign=\"top\">1188-VO-SN-NIANG</th>\n",
+       "      <th rowspan=\"3\" valign=\"top\">1188-VO-NIANG-NIEL-SN-2304-VMF00259</th>\n",
+       "      <th rowspan=\"3\" valign=\"top\">Senegal</th>\n",
+       "      <th>2020</th>\n",
+       "      <td>11</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2021</th>\n",
+       "      <td>16</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2022</th>\n",
+       "      <td>44</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1330-VO-GN-LAMA</th>\n",
+       "      <th>1330-VO-GN-LAMA-VMF00250</th>\n",
+       "      <th>Guinea</th>\n",
+       "      <th>2022</th>\n",
+       "      <td>196</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1354-VO-KE-DONNELLY</th>\n",
+       "      <th>1354-VO-KE-DONNELLY-VMF00281</th>\n",
+       "      <th>Kenya</th>\n",
+       "      <th>2023</th>\n",
+       "      <td>466</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "taxon                                                                 funestus\n",
+       "study_id            sample_set                          country year          \n",
+       "1188-VO-SN-NIANG    1188-VO-NIANG-NIEL-SN-2304-VMF00259 Senegal 2020        11\n",
+       "                                                                2021        16\n",
+       "                                                                2022        44\n",
+       "1330-VO-GN-LAMA     1330-VO-GN-LAMA-VMF00250            Guinea  2022       196\n",
+       "1354-VO-KE-DONNELLY 1354-VO-KE-DONNELLY-VMF00281        Kenya   2023       466"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df_samples = af1.sample_metadata(sample_sets=\"1.4\")\n",
+    "df_summary = df_samples.pivot_table(\n",
+    "    index=[\"study_id\",\"sample_set\", \"country\", \"year\"], \n",
+    "    columns=[\"taxon\"],\n",
+    "    values=\"sample_id\", \n",
+    "    aggfunc=len,\n",
+    "    fill_value=0)\n",
+    "df_summary"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "id": "dLiU0ulIpk8p"
+   },
+   "source": [
+    "Note that there can be multiple sampling sites represented within the same sample set."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "id": "OToX5vhfpk8p"
+   },
+   "source": [
+    "## Further reading\n",
+    "\n",
+    "We hope this page has provided a useful introduction to the `Af1.4` data resource. If you would like to start working with these data, please visit the [cloud data access guide](cloud) or the [data download guide](download) or continue browsing the other documentation on this site.\n",
+    "\n",
+    "If you have any questions about the data and how to use them, please do get in touch by [starting a new discussion](https://github.com/malariagen/vector-data/discussions/new) on the malariagen/vector-data repository on GitHub."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "celltoolbar": "Tags",
+  "colab": {
+   "name": "Ag3.0-intro.ipynb",
+   "provenance": []
+  },
+  "kernelspec": {
+   "display_name": "global-global-mgenv-5.1.0",
+   "language": "python",
+   "name": "conda-env-global-global-mgenv-5.1.0-py"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/af1/af1.4.html b/af1/af1.4.html
new file mode 100644
index 0000000..e347548
--- /dev/null
+++ b/af1/af1.4.html
@@ -0,0 +1,1196 @@
+
+<!DOCTYPE html>
+
+<html>
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
+    <title>Af1.4 &#8212; MalariaGEN vector data user guide</title>
+    
+  <!-- Loaded before other Sphinx assets -->
+  <link href="../_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
+<link href="../_static/styles/pydata-sphinx-theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
+
+    
+  <link rel="stylesheet"
+    href="../_static/vendor/fontawesome/5.13.0/css/all.min.css">
+  <link rel="preload" as="font" type="font/woff2" crossorigin
+    href="../_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
+  <link rel="preload" as="font" type="font/woff2" crossorigin
+    href="../_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
+
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
+    <link rel="stylesheet" href="../_static/styles/sphinx-book-theme.css?digest=5115cc725059bd94278eecd172e13a965bf8f5a9" type="text/css" />
+    <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/copybutton.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/mystnb.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/sphinx-thebe.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/myfile.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/design-style.b7bb847fb20b106c3d81b95245e65545.min.css" />
+    
+  <!-- Pre-loaded scripts that we'll load fully later -->
+  <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf">
+
+    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+    <script src="../_static/jquery.js"></script>
+    <script src="../_static/underscore.js"></script>
+    <script src="../_static/doctools.js"></script>
+    <script src="../_static/clipboard.min.js"></script>
+    <script src="../_static/copybutton.js"></script>
+    <script src="../_static/scripts/sphinx-book-theme.js?digest=9c920249402e914e316237a7dbc6769907cce411"></script>
+    <script>let toggleHintShow = 'Click to show';</script>
+    <script>let toggleHintHide = 'Click to hide';</script>
+    <script>let toggleOpenOnPrint = 'true';</script>
+    <script src="../_static/togglebutton.js"></script>
+    <script kind="utterances">
+
+    var commentsRunWhenDOMLoaded = cb => {
+    if (document.readyState != 'loading') {
+        cb()
+    } else if (document.addEventListener) {
+        document.addEventListener('DOMContentLoaded', cb)
+    } else {
+        document.attachEvent('onreadystatechange', function() {
+        if (document.readyState == 'complete') cb()
+        })
+    }
+}
+
+var addUtterances = () => {
+    var script = document.createElement("script");
+    script.type = "text/javascript";
+    script.src = "https://utteranc.es/client.js";
+    script.async = "async";
+
+    script.setAttribute("repo", "malariagen/vector-data");
+    script.setAttribute("issue-term", "pathname");
+    script.setAttribute("theme", "github-light");
+    script.setAttribute("label", "comment");
+    script.setAttribute("crossorigin", "anonymous");
+
+    sections = document.querySelectorAll("div.section");
+    if (sections !== null) {
+        section = sections[sections.length-1];
+        section.appendChild(script);
+    }
+}
+commentsRunWhenDOMLoaded(addUtterances);
+</script>
+    <script>var togglebuttonSelector = '.toggle, .admonition.dropdown, .tag_hide_input div.cell_input, .tag_hide-input div.cell_input, .tag_hide_output div.cell_output, .tag_hide-output div.cell_output, .tag_hide_cell.cell, .tag_hide-cell.cell';</script>
+    <script src="../_static/design-tabs.js"></script>
+    <script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"
+const thebe_selector = ".thebe,.cell"
+const thebe_selector_input = "pre"
+const thebe_selector_output = ".output, .cell_output"
+</script>
+    <script async="async" src="../_static/sphinx-thebe.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="docsearch:language" content="None">
+    
+
+    <!-- Google Analytics -->
+    
+  </head>
+  <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="60">
+<!-- Checkboxes to toggle the left sidebar -->
+<input type="checkbox" class="sidebar-toggle" name="__navigation" id="__navigation" aria-label="Toggle navigation sidebar">
+<label class="overlay overlay-navbar" for="__navigation">
+    <div class="visually-hidden">Toggle navigation sidebar</div>
+</label>
+<!-- Checkboxes to toggle the in-page toc -->
+<input type="checkbox" class="sidebar-toggle" name="__page-toc" id="__page-toc" aria-label="Toggle in-page Table of Contents">
+<label class="overlay overlay-pagetoc" for="__page-toc">
+    <div class="visually-hidden">Toggle in-page Table of Contents</div>
+</label>
+<!-- Headers at the top -->
+<div class="announcement header-item noprint"></div>
+<div class="header header-item noprint"></div>
+
+    
+    <div class="container-fluid" id="banner"></div>
+
+    
+
+    <div class="container-xl">
+      <div class="row">
+          
+<!-- Sidebar -->
+<div class="bd-sidebar noprint" id="site-navigation">
+    <div class="bd-sidebar__content">
+        <div class="bd-sidebar__top"><div class="navbar-brand-box">
+    <a class="navbar-brand text-wrap" href="../index.html">
+      
+        <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 -->
+        
+      
+      
+      <img src="../_static/logo.png" class="logo" alt="logo">
+      
+      
+      <h1 class="site-logo" id="site-title">MalariaGEN vector data user guide</h1>
+      
+    </a>
+</div><form class="bd-search d-flex align-items-center" action="../search.html" method="get">
+  <i class="icon fas fa-search"></i>
+  <input type="search" class="form-control" name="q" id="search-input" placeholder="Search this book..." aria-label="Search this book..." autocomplete="off" >
+</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
+    <div class="bd-toc-item active">
+        
+        <ul class="nav bd-sidenav bd-sidenav__home-link">
+            <li class="toctree-l1">
+                <a class="reference internal" href="../landing-page.html">
+                    MalariaGEN vector data user guide
+                </a>
+            </li>
+        </ul>
+        <p aria-level="2" class="caption" role="heading">
+ <span class="caption-text">
+  Malaria Vector Genome Observatory
+ </span>
+</p>
+<ul class="nav bd-sidenav">
+ <li class="toctree-l1">
+  <a class="reference internal" href="../vobs/vobs-data-access.html">
+   Vector Observatory Data Access
+  </a>
+ </li>
+</ul>
+<p aria-level="2" class="caption" role="heading">
+ <span class="caption-text">
+  Anopheles gambiae complex
+ </span>
+</p>
+<ul class="nav bd-sidenav">
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.0.html">
+   Ag3.0 (Ag1000G phase 3)
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.1.html">
+   Ag3.1
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.2.html">
+   Ag3.2
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.3.html">
+   Ag3.3
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.4.html">
+   Ag3.4
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.5.html">
+   Ag3.5
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.6.html">
+   Ag3.6
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.7.html">
+   Ag3.7
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.8.html">
+   Ag3.8
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.9.html">
+   Ag3.9
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/ag3.10.html">
+   Ag3.10
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/cloud.html">
+   Ag3 cloud data access
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/download.html">
+   Ag3 data downloads
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/methods.html">
+   Ag3 sequencing and variant calling methods
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/api.html">
+   Ag3 API
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../ag3/analysis.html">
+   Ag3 analysis
+  </a>
+ </li>
+</ul>
+<p aria-level="2" class="caption" role="heading">
+ <span class="caption-text">
+  Anopheles funestus
+ </span>
+</p>
+<ul class="nav bd-sidenav">
+ <li class="toctree-l1">
+  <a class="reference internal" href="af1.0.html">
+   Af1.0  (
+   <em>
+    Anopheles funestus
+   </em>
+   Project Phase 1 Data Release)
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="af1.1.html">
+   Af1.1
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="af1.2.html">
+   Af1.2
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="af1.3.html">
+   Af1.3
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="cloud.html">
+   Af1 cloud data access
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="download.html">
+   Af1 data downloads
+  </a>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="api.html">
+   Af1 API
+  </a>
+ </li>
+</ul>
+<p aria-level="2" class="caption" role="heading">
+ <span class="caption-text">
+  Anopheles minimus
+ </span>
+</p>
+<ul class="nav bd-sidenav">
+ <li class="toctree-l1 has-children">
+  <a class="reference internal" href="../amin1/intro.html">
+   Amin1.0
+  </a>
+  <input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/>
+  <label for="toctree-checkbox-1">
+   <i class="fas fa-chevron-down">
+   </i>
+  </label>
+  <ul>
+   <li class="toctree-l2">
+    <a class="reference internal" href="../amin1/cloud.html">
+     Amin1.0 cloud data access
+    </a>
+   </li>
+   <li class="toctree-l2">
+    <a class="reference internal" href="../amin1/download.html">
+     Amin1.0 data downloads
+    </a>
+   </li>
+  </ul>
+ </li>
+ <li class="toctree-l1">
+  <a class="reference internal" href="../amin1/api.html">
+   Amin1 API
+  </a>
+ </li>
+</ul>
+<p aria-level="2" class="caption" role="heading">
+ <span class="caption-text">
+  Partners and community
+ </span>
+</p>
+<ul class="nav bd-sidenav">
+ <li class="toctree-l1">
+  <a class="reference internal" href="../studies-ag1000g.html">
+   Ag1000G partner studies
+  </a>
+ </li>
+</ul>
+<p aria-level="2" class="caption" role="heading">
+ <span class="caption-text">
+  Release notes
+ </span>
+</p>
+<ul class="nav bd-sidenav">
+ <li class="toctree-l1">
+  <a class="reference internal" href="../release-notes.html">
+   Release notes
+  </a>
+ </li>
+</ul>
+
+    </div>
+</nav></div>
+        <div class="bd-sidebar__bottom">
+             <!-- To handle the deprecated key -->
+            
+            <div class="navbar_extra_footer">
+            Powered by <a href="https://jupyterbook.org">Jupyter Book</a>
+            </div>
+            
+        </div>
+    </div>
+    <div id="rtd-footer-container"></div>
+</div>
+
+
+          
+
+
+          
+<!-- A tiny helper pixel to detect if we've scrolled -->
+<div class="sbt-scroll-pixel-helper"></div>
+<!-- Main content -->
+<div class="col py-0 content-container">
+    
+    <div class="header-article row sticky-top noprint">
+        
+
+
+
+<div class="col py-1 d-flex header-article-main">
+    <div class="header-article__left">
+        
+        <label for="__navigation"
+  class="headerbtn"
+  data-toggle="tooltip"
+data-placement="right"
+title="Toggle navigation"
+>
+  
+
+<span class="headerbtn__icon-container">
+  <i class="fas fa-bars"></i>
+  </span>
+
+</label>
+
+        
+    </div>
+    <div class="header-article__right">
+<div class="menu-dropdown menu-dropdown-launch-buttons">
+  <button class="headerbtn menu-dropdown__trigger"
+      aria-label="Launch interactive content">
+      <i class="fas fa-rocket"></i>
+  </button>
+  <div class="menu-dropdown__content">
+    <ul>
+      <li>
+        <a href="https://gke.mybinder.org/v2/gh/malariagen/vector-data/master?urlpath=lab/tree/docs/af1/af1.4.ipynb"
+   class="headerbtn"
+   data-toggle="tooltip"
+data-placement="left"
+title="Launch on Binder"
+>
+  
+
+<span class="headerbtn__icon-container">
+  
+    <img src="../_static/images/logo_binder.svg">
+  </span>
+<span class="headerbtn__text-container">Binder</span>
+</a>
+
+      </li>
+      
+      <li>
+        <a href="https://colab.research.google.com/github/malariagen/vector-data/blob/master/docs/af1/af1.4.ipynb"
+   class="headerbtn"
+   data-toggle="tooltip"
+data-placement="left"
+title="Launch on Colab"
+>
+  
+
+<span class="headerbtn__icon-container">
+  
+    <img src="../_static/images/logo_colab.png">
+  </span>
+<span class="headerbtn__text-container">Colab</span>
+</a>
+
+      </li>
+      
+    </ul>
+  </div>
+</div>
+
+<button onclick="toggleFullScreen()"
+  class="headerbtn"
+  data-toggle="tooltip"
+data-placement="bottom"
+title="Fullscreen mode"
+>
+  
+
+<span class="headerbtn__icon-container">
+  <i class="fas fa-expand"></i>
+  </span>
+
+</button>
+
+<div class="menu-dropdown menu-dropdown-repository-buttons">
+  <button class="headerbtn menu-dropdown__trigger"
+      aria-label="Source repositories">
+      <i class="fab fa-github"></i>
+  </button>
+  <div class="menu-dropdown__content">
+    <ul>
+      <li>
+        <a href="https://github.com/malariagen/vector-data"
+   class="headerbtn"
+   data-toggle="tooltip"
+data-placement="left"
+title="Source repository"
+>
+  
+
+<span class="headerbtn__icon-container">
+  <i class="fab fa-github"></i>
+  </span>
+<span class="headerbtn__text-container">repository</span>
+</a>
+
+      </li>
+      
+      <li>
+        <a href="https://github.com/malariagen/vector-data/issues/new?title=Issue%20on%20page%20%2Faf1/af1.4.html&body=Your%20issue%20content%20here."
+   class="headerbtn"
+   data-toggle="tooltip"
+data-placement="left"
+title="Open an issue"
+>
+  
+
+<span class="headerbtn__icon-container">
+  <i class="fas fa-lightbulb"></i>
+  </span>
+<span class="headerbtn__text-container">open issue</span>
+</a>
+
+      </li>
+      
+    </ul>
+  </div>
+</div>
+
+<div class="menu-dropdown menu-dropdown-download-buttons">
+  <button class="headerbtn menu-dropdown__trigger"
+      aria-label="Download this page">
+      <i class="fas fa-download"></i>
+  </button>
+  <div class="menu-dropdown__content">
+    <ul>
+      <li>
+        <a href="../_sources/af1/af1.4.ipynb"
+   class="headerbtn"
+   data-toggle="tooltip"
+data-placement="left"
+title="Download source file"
+>
+  
+
+<span class="headerbtn__icon-container">
+  <i class="fas fa-file"></i>
+  </span>
+<span class="headerbtn__text-container">.ipynb</span>
+</a>
+
+      </li>
+      
+      <li>
+        
+<button onclick="printPdf(this)"
+  class="headerbtn"
+  data-toggle="tooltip"
+data-placement="left"
+title="Print to PDF"
+>
+  
+
+<span class="headerbtn__icon-container">
+  <i class="fas fa-file-pdf"></i>
+  </span>
+<span class="headerbtn__text-container">.pdf</span>
+</button>
+
+      </li>
+      
+    </ul>
+  </div>
+</div>
+<label for="__page-toc"
+  class="headerbtn headerbtn-page-toc"
+  
+>
+  
+
+<span class="headerbtn__icon-container">
+  <i class="fas fa-list"></i>
+  </span>
+
+</label>
+
+    </div>
+</div>
+
+<!-- Table of contents -->
+<div class="col-md-3 bd-toc show noprint">
+    <div class="tocsection onthispage pt-5 pb-3">
+        <i class="fas fa-list"></i> Contents
+    </div>
+    <nav id="bd-toc-nav" aria-label="Page">
+        <ul class="visible nav section-nav flex-column">
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#terms-of-use">
+   Terms of use
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#partner-studies">
+   Partner studies
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#whole-genome-sequencing-and-variant-calling">
+   Whole-genome sequencing and variant calling
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#data-hosting">
+   Data hosting
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#sample-sets">
+   Sample sets
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#further-reading">
+   Further reading
+  </a>
+ </li>
+</ul>
+
+    </nav>
+</div>
+    </div>
+    <div class="article row">
+        <div class="col pl-md-3 pl-lg-5 content-container">
+            <!-- Table of contents that is only displayed when printing the page -->
+            <div id="jb-print-docs-body" class="onlyprint">
+                <h1>Af1.4</h1>
+                <!-- Table of contents -->
+                <div id="print-main-content">
+                    <div id="jb-print-toc">
+                        
+                        <div>
+                            <h2> Contents </h2>
+                        </div>
+                        <nav aria-label="Page">
+                            <ul class="visible nav section-nav flex-column">
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#terms-of-use">
+   Terms of use
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#partner-studies">
+   Partner studies
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#whole-genome-sequencing-and-variant-calling">
+   Whole-genome sequencing and variant calling
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#data-hosting">
+   Data hosting
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#sample-sets">
+   Sample sets
+  </a>
+ </li>
+ <li class="toc-h2 nav-item toc-entry">
+  <a class="reference internal nav-link" href="#further-reading">
+   Further reading
+  </a>
+ </li>
+</ul>
+
+                        </nav>
+                    </div>
+                </div>
+            </div>
+            <main id="main-content" role="main">
+                
+              <div>
+                
+  <section class="tex2jax_ignore mathjax_ignore" id="af1-4">
+<h1>Af1.4<a class="headerlink" href="#af1-4" title="Permalink to this headline">#</a></h1>
+<p>The <strong><a class="reference internal" href="#"><span class="doc std std-doc">Af1.4</span></a>:  <em>Anopheles gambiae</em> data resource</strong> contains single nucleotide polymorphism (SNP) calls and SNP haplotypes from whole-genome sequencing of 733 mosquitoes.</p>
+<p>More information about this release can be found in the <a class="reference external" href="https://www.malariagen.net/data_package/af14-anopheles-funestus-data-resource/">data resource website</a>.</p>
+<p>This page provides an introduction to open data resources released as part of <code class="docutils literal notranslate"><span class="pre">Af1.4</span></code>.</p>
+<p>If you have any questions about this guide or how to use the data, please <a class="reference external" href="https://github.com/malariagen/vector-public-data/discussions/new">start a new discussion</a> on the malariagen/vector-open-data repo on GitHub. If you find any bugs, please <a class="reference external" href="https://github.com/malariagen/vector-public-data/issues/new/choose">raise an issue</a>.</p>
+<section id="terms-of-use">
+<h2>Terms of use<a class="headerlink" href="#terms-of-use" title="Permalink to this headline">#</a></h2>
+<p>Data from this project will be made publicly available before journal publication. Unless otherwise stated, analyses of project data are ongoing and publications are in preparation by project partners, and it is not permitted to use project data for publication (including any type of communication with the general public) without prior permission from the originating partner studies.</p>
+<p>Although malaria is generally an endemic rather than an epidemic disease, and the focus of this project is on surveillance of disease vectors rather than pathogens, our data terms of use build on MalariaGEN’s approach to data sharing, and adopt norms which have been established for rapid sharing of pathogen genomic data during disease outbreaks. The primary rationale for this approach is that malaria remains a public health emergency, where ethically appropriate and rapid sharing of genomic surveillance data can help to detect and respond to biological threats such as new forms of insecticide resistance, and to adapt malaria vector control strategies to different settings and changing circumstances.</p>
+<p>The publication embargo for all data on this release will expire on the <strong>16th of August 2026</strong>.</p>
+<p>If you have any questions about the terms of use, please email <a class="reference external" href="mailto:support&#37;&#52;&#48;malariagen&#46;net">support<span>&#64;</span>malariagen<span>&#46;</span>net</a></p>
+</section>
+<section id="partner-studies">
+<h2>Partner studies<a class="headerlink" href="#partner-studies" title="Permalink to this headline">#</a></h2>
+<ul class="simple">
+<li><p><a class="reference external" href="https://www.malariagen.net/network/where-we-work/1188-VO-SN-NIANG">1188-VO-SN-NIANG</a> - <em>Anopheles gambiae</em> vector surveillance in Senegal.</p></li>
+<li><p><a class="reference external" href="https://www.malariagen.net/network/where-we-work/1330-VO-GN-LAMA">1330-VO-GN-LAMA</a> - <em>Anopheles gambiae</em> vector surveillance in Guinea.</p></li>
+<li><p><a class="reference external" href="https://www.malariagen.net/network/where-we-work/1354-VO-KE-DONNELLY">1354-VO-KE-DONNELLY</a> - <em>Anopheles</em> vector surveillance in Kenya.</p></li>
+</ul>
+</section>
+<section id="whole-genome-sequencing-and-variant-calling">
+<h2>Whole-genome sequencing and variant calling<a class="headerlink" href="#whole-genome-sequencing-and-variant-calling" title="Permalink to this headline">#</a></h2>
+<p>All samples in <code class="docutils literal notranslate"><span class="pre">Af1.4</span></code> have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis.</p>
+</section>
+<section id="data-hosting">
+<h2>Data hosting<a class="headerlink" href="#data-hosting" title="Permalink to this headline">#</a></h2>
+<p>Data from <code class="docutils literal notranslate"><span class="pre">Af1.4</span></code> are hosted by several different services.</p>
+<p>The SNP data have also been uploaded to Google Cloud, and can be analysed directly within the cloud without having to download or copy any data, including via free interactive computing services such as <a class="reference external" href="https://gke.mybinder.org/">MyBinder</a> and <a class="reference external" href="https://colab.research.google.com/">Google Colab</a>. Further information about analysing these data in the cloud is provided in the <a class="reference internal" href="cloud.html"><span class="doc std std-doc">cloud data access guide</span></a>.</p>
+</section>
+<section id="sample-sets">
+<h2>Sample sets<a class="headerlink" href="#sample-sets" title="Permalink to this headline">#</a></h2>
+<p>The samples included in <code class="docutils literal notranslate"><span class="pre">Af1.4</span></code> have been organised into 1 sample set.</p>
+<p>Each sample set corresponds to a set of mosquito specimens from a contributing study. Study details can be found in the partner studies webpages listed above.</p>
+<div class="cell tag_remove-input docutils container">
+</div>
+<p><strong>Note:</strong> To access the <code class="docutils literal notranslate"><span class="pre">Af1.4</span></code> release, you need to use the <code class="docutils literal notranslate"><span class="pre">pre=True</span></code> flag.</p>
+<p>This flag is used when more data will be added to this release, for the case of <code class="docutils literal notranslate"><span class="pre">Af1.4</span></code>, CNV data for the sample sets on this release will be included at a future date.</p>
+<div class="cell tag_remove-input docutils container">
+<div class="cell_output docutils container">
+<script type="application/javascript">'use strict';
+(function(root) {
+  function now() {
+    return new Date();
+  }
+
+  const force = true;
+
+  if (typeof root._bokeh_onload_callbacks === "undefined" || force === true) {
+    root._bokeh_onload_callbacks = [];
+    root._bokeh_is_loading = undefined;
+  }
+
+const JS_MIME_TYPE = 'application/javascript';
+  const HTML_MIME_TYPE = 'text/html';
+  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';
+  const CLASS_NAME = 'output_bokeh rendered_html';
+
+  /**
+   * Render data to the DOM node
+   */
+  function render(props, node) {
+    const script = document.createElement("script");
+    node.appendChild(script);
+  }
+
+  /**
+   * Handle when an output is cleared or removed
+   */
+  function handleClearOutput(event, handle) {
+    function drop(id) {
+      const view = Bokeh.index.get_by_id(id)
+      if (view != null) {
+        view.model.document.clear()
+        Bokeh.index.delete(view)
+      }
+    }
+
+    const cell = handle.cell;
+
+    const id = cell.output_area._bokeh_element_id;
+    const server_id = cell.output_area._bokeh_server_id;
+
+    // Clean up Bokeh references
+    if (id != null) {
+      drop(id)
+    }
+
+    if (server_id !== undefined) {
+      // Clean up Bokeh references
+      const cmd_clean = "from bokeh.io.state import curstate; print(curstate().uuid_to_server['" + server_id + "'].get_sessions()[0].document.roots[0]._id)";
+      cell.notebook.kernel.execute(cmd_clean, {
+        iopub: {
+          output: function(msg) {
+            const id = msg.content.text.trim()
+            drop(id)
+          }
+        }
+      });
+      // Destroy server and session
+      const cmd_destroy = "import bokeh.io.notebook as ion; ion.destroy_server('" + server_id + "')";
+      cell.notebook.kernel.execute(cmd_destroy);
+    }
+  }
+
+  /**
+   * Handle when a new output is added
+   */
+  function handleAddOutput(event, handle) {
+    const output_area = handle.output_area;
+    const output = handle.output;
+
+    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only
+    if ((output.output_type != "display_data") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {
+      return
+    }
+
+    const toinsert = output_area.element.find("." + CLASS_NAME.split(' ')[0]);
+
+    if (output.metadata[EXEC_MIME_TYPE]["id"] !== undefined) {
+      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];
+      // store reference to embed id on output_area
+      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE]["id"];
+    }
+    if (output.metadata[EXEC_MIME_TYPE]["server_id"] !== undefined) {
+      const bk_div = document.createElement("div");
+      bk_div.innerHTML = output.data[HTML_MIME_TYPE];
+      const script_attrs = bk_div.children[0].attributes;
+      for (let i = 0; i < script_attrs.length; i++) {
+        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);
+        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent
+      }
+      // store reference to server id on output_area
+      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE]["server_id"];
+    }
+  }
+
+  function register_renderer(events, OutputArea) {
+
+    function append_mime(data, metadata, element) {
+      // create a DOM node to render to
+      const toinsert = this.create_output_subarea(
+        metadata,
+        CLASS_NAME,
+        EXEC_MIME_TYPE
+      );
+      this.keyboard_manager.register_events(toinsert);
+      // Render to node
+      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};
+      render(props, toinsert[toinsert.length - 1]);
+      element.append(toinsert);
+      return toinsert
+    }
+
+    /* Handle when an output is cleared or removed */
+    events.on('clear_output.CodeCell', handleClearOutput);
+    events.on('delete.Cell', handleClearOutput);
+
+    /* Handle when a new output is added */
+    events.on('output_added.OutputArea', handleAddOutput);
+
+    /**
+     * Register the mime type and append_mime function with output_area
+     */
+    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {
+      /* Is output safe? */
+      safe: true,
+      /* Index of renderer in `output_area.display_order` */
+      index: 0
+    });
+  }
+
+  // register the mime type if in Jupyter Notebook environment and previously unregistered
+  if (root.Jupyter !== undefined) {
+    const events = require('base/js/events');
+    const OutputArea = require('notebook/js/outputarea').OutputArea;
+
+    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {
+      register_renderer(events, OutputArea);
+    }
+  }
+  if (typeof (root._bokeh_timeout) === "undefined" || force === true) {
+    root._bokeh_timeout = Date.now() + 5000;
+    root._bokeh_failed_load = false;
+  }
+
+  const NB_LOAD_WARNING = {'data': {'text/html':
+     "<div style='background-color: #fdd'>\n"+
+     "<p>\n"+
+     "BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \n"+
+     "may be due to a slow or bad network connection. Possible fixes:\n"+
+     "</p>\n"+
+     "<ul>\n"+
+     "<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\n"+
+     "<li>use INLINE resources instead, as so:</li>\n"+
+     "</ul>\n"+
+     "<code>\n"+
+     "from bokeh.resources import INLINE\n"+
+     "output_notebook(resources=INLINE)\n"+
+     "</code>\n"+
+     "</div>"}};
+
+  function display_loaded(error = null) {
+    const el = document.getElementById(null);
+    if (el != null) {
+      const html = (() => {
+        if (typeof root.Bokeh === "undefined") {
+          if (error == null) {
+            return "BokehJS is loading ...";
+          } else {
+            return "BokehJS failed to load.";
+          }
+        } else {
+          const prefix = `BokehJS ${root.Bokeh.version}`;
+          if (error == null) {
+            return `${prefix} successfully loaded.`;
+          } else {
+            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;
+          }
+        }
+      })();
+      el.innerHTML = html;
+
+      if (error != null) {
+        const wrapper = document.createElement("div");
+        wrapper.style.overflow = "auto";
+        wrapper.style.height = "5em";
+        wrapper.style.resize = "vertical";
+        const content = document.createElement("div");
+        content.style.fontFamily = "monospace";
+        content.style.whiteSpace = "pre-wrap";
+        content.style.backgroundColor = "rgb(255, 221, 221)";
+        content.textContent = error.stack ?? error.toString();
+        wrapper.append(content);
+        el.append(wrapper);
+      }
+    } else if (Date.now() < root._bokeh_timeout) {
+      setTimeout(() => display_loaded(error), 100);
+    }
+  }
+
+  function run_callbacks() {
+    try {
+      root._bokeh_onload_callbacks.forEach(function(callback) {
+        if (callback != null)
+          callback();
+      });
+    } finally {
+      delete root._bokeh_onload_callbacks
+    }
+    console.debug("Bokeh: all callbacks have finished");
+  }
+
+  function load_libs(css_urls, js_urls, callback) {
+    if (css_urls == null) css_urls = [];
+    if (js_urls == null) js_urls = [];
+
+    root._bokeh_onload_callbacks.push(callback);
+    if (root._bokeh_is_loading > 0) {
+      console.debug("Bokeh: BokehJS is being loaded, scheduling callback at", now());
+      return null;
+    }
+    if (js_urls == null || js_urls.length === 0) {
+      run_callbacks();
+      return null;
+    }
+    console.debug("Bokeh: BokehJS not loaded, scheduling load and callback at", now());
+    root._bokeh_is_loading = css_urls.length + js_urls.length;
+
+    function on_load() {
+      root._bokeh_is_loading--;
+      if (root._bokeh_is_loading === 0) {
+        console.debug("Bokeh: all BokehJS libraries/stylesheets loaded");
+        run_callbacks()
+      }
+    }
+
+    function on_error(url) {
+      console.error("failed to load " + url);
+    }
+
+    for (let i = 0; i < css_urls.length; i++) {
+      const url = css_urls[i];
+      const element = document.createElement("link");
+      element.onload = on_load;
+      element.onerror = on_error.bind(null, url);
+      element.rel = "stylesheet";
+      element.type = "text/css";
+      element.href = url;
+      console.debug("Bokeh: injecting link tag for BokehJS stylesheet: ", url);
+      document.body.appendChild(element);
+    }
+
+    for (let i = 0; i < js_urls.length; i++) {
+      const url = js_urls[i];
+      const element = document.createElement('script');
+      element.onload = on_load;
+      element.onerror = on_error.bind(null, url);
+      element.async = false;
+      element.src = url;
+      console.debug("Bokeh: injecting script tag for BokehJS library: ", url);
+      document.head.appendChild(element);
+    }
+  };
+
+  function inject_raw_css(css) {
+    const element = document.createElement("style");
+    element.appendChild(document.createTextNode(css));
+    document.body.appendChild(element);
+  }
+
+  const js_urls = ["https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js", "https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.1.min.js", "https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.1.min.js", "https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.1.min.js", "https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.1.min.js"];
+  const css_urls = [];
+
+  const inline_js = [    function(Bokeh) {
+      Bokeh.set_log_level("info");
+    },
+function(Bokeh) {
+    }
+  ];
+
+  function run_inline_js() {
+    if (root.Bokeh !== undefined || force === true) {
+      try {
+            for (let i = 0; i < inline_js.length; i++) {
+      inline_js[i].call(root, root.Bokeh);
+    }
+
+      } catch (error) {throw error;
+      }} else if (Date.now() < root._bokeh_timeout) {
+      setTimeout(run_inline_js, 100);
+    } else if (!root._bokeh_failed_load) {
+      console.log("Bokeh: BokehJS failed to load within specified timeout.");
+      root._bokeh_failed_load = true;
+    } else if (force !== true) {
+      const cell = $(document.getElementById(null)).parents('.cell').data().cell;
+      cell.output_area.append_execute_result(NB_LOAD_WARNING)
+    }
+  }
+
+  if (root._bokeh_is_loading === 0) {
+    console.debug("Bokeh: BokehJS loaded, going straight to plotting");
+    run_inline_js();
+  } else {
+    load_libs(css_urls, js_urls, function() {
+      console.debug("Bokeh: BokehJS plotting callback run at", now());
+      run_inline_js();
+    });
+  }
+}(window));</script></div>
+</div>
+<div class="cell tag_remove-input docutils container">
+<div class="cell_output docutils container">
+<div class="output text_html"><div>
+<style scoped>
+    .dataframe tbody tr th:only-of-type {
+        vertical-align: middle;
+    }
+
+    .dataframe tbody tr th {
+        vertical-align: top;
+    }
+
+    .dataframe thead th {
+        text-align: right;
+    }
+</style>
+<table border="1" class="dataframe">
+  <thead>
+    <tr style="text-align: right;">
+      <th></th>
+      <th>sample_set</th>
+      <th>sample_count</th>
+    </tr>
+    <tr>
+      <th>study_id</th>
+      <th></th>
+      <th></th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <th>1188-VO-SN-NIANG</th>
+      <td>1188-VO-NIANG-NIEL-SN-2304-VMF00259</td>
+      <td>71</td>
+    </tr>
+    <tr>
+      <th>1330-VO-GN-LAMA</th>
+      <td>1330-VO-GN-LAMA-VMF00250</td>
+      <td>196</td>
+    </tr>
+    <tr>
+      <th>1354-VO-KE-DONNELLY</th>
+      <td>1354-VO-KE-DONNELLY-VMF00281</td>
+      <td>466</td>
+    </tr>
+  </tbody>
+</table>
+</div></div></div>
+</div>
+<p>Here is a more detailed breakdown of the samples contained within this sample set, summarised by country, year of collection, and species:</p>
+<div class="cell tag_remove-input docutils container">
+<div class="cell_output docutils container">
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>                                     
+</pre></div>
+</div>
+<div class="output text_html"><div>
+<style scoped>
+    .dataframe tbody tr th:only-of-type {
+        vertical-align: middle;
+    }
+
+    .dataframe tbody tr th {
+        vertical-align: top;
+    }
+
+    .dataframe thead th {
+        text-align: right;
+    }
+</style>
+<table border="1" class="dataframe">
+  <thead>
+    <tr style="text-align: right;">
+      <th></th>
+      <th></th>
+      <th></th>
+      <th>taxon</th>
+      <th>funestus</th>
+    </tr>
+    <tr>
+      <th>study_id</th>
+      <th>sample_set</th>
+      <th>country</th>
+      <th>year</th>
+      <th></th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <th rowspan="3" valign="top">1188-VO-SN-NIANG</th>
+      <th rowspan="3" valign="top">1188-VO-NIANG-NIEL-SN-2304-VMF00259</th>
+      <th rowspan="3" valign="top">Senegal</th>
+      <th>2020</th>
+      <td>11</td>
+    </tr>
+    <tr>
+      <th>2021</th>
+      <td>16</td>
+    </tr>
+    <tr>
+      <th>2022</th>
+      <td>44</td>
+    </tr>
+    <tr>
+      <th>1330-VO-GN-LAMA</th>
+      <th>1330-VO-GN-LAMA-VMF00250</th>
+      <th>Guinea</th>
+      <th>2022</th>
+      <td>196</td>
+    </tr>
+    <tr>
+      <th>1354-VO-KE-DONNELLY</th>
+      <th>1354-VO-KE-DONNELLY-VMF00281</th>
+      <th>Kenya</th>
+      <th>2023</th>
+      <td>466</td>
+    </tr>
+  </tbody>
+</table>
+</div></div></div>
+</div>
+<p>Note that there can be multiple sampling sites represented within the same sample set.</p>
+</section>
+<section id="further-reading">
+<h2>Further reading<a class="headerlink" href="#further-reading" title="Permalink to this headline">#</a></h2>
+<p>We hope this page has provided a useful introduction to the <code class="docutils literal notranslate"><span class="pre">Af1.4</span></code> data resource. If you would like to start working with these data, please visit the <a class="reference internal" href="cloud.html"><span class="doc std std-doc">cloud data access guide</span></a> or the <a class="reference internal" href="download.html"><span class="doc std std-doc">data download guide</span></a> or continue browsing the other documentation on this site.</p>
+<p>If you have any questions about the data and how to use them, please do get in touch by <a class="reference external" href="https://github.com/malariagen/vector-data/discussions/new">starting a new discussion</a> on the malariagen/vector-data repository on GitHub.</p>
+</section>
+</section>
+
+    <script type="text/x-thebe-config">
+    {
+        requestKernel: true,
+        binderOptions: {
+            repo: "binder-examples/jupyter-stacks-datascience",
+            ref: "master",
+        },
+        codeMirrorConfig: {
+            theme: "abcdef",
+            mode: "conda-env-global-global-mgenv-5.1.0-py"
+        },
+        kernelOptions: {
+            kernelName: "conda-env-global-global-mgenv-5.1.0-py",
+            path: "./af1"
+        },
+        predefinedOutput: true
+    }
+    </script>
+    <script>kernelName = 'conda-env-global-global-mgenv-5.1.0-py'</script>
+
+              </div>
+              
+            </main>
+            <footer class="footer-article noprint">
+                
+    <!-- Previous / next buttons -->
+<div class='prev-next-area'>
+</div>
+            </footer>
+        </div>
+    </div>
+    <div class="footer-content row">
+        <footer class="col footer"><p>
+  
+    By MalariaGEN<br/>
+  
+      &copy; Copyright 2021.<br/>
+</p>
+        </footer>
+    </div>
+    
+</div>
+
+
+      </div>
+    </div>
+  
+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
+  <script src="../_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf"></script>
+
+
+  </body>
+</html>
\ No newline at end of file
diff --git a/objects.inv b/objects.inv
index 9b42e1d..ce0930a 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index 630bec7..fe94bcc 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["af1/af1.0","af1/af1.1","af1/af1.2","af1/af1.3","af1/api","af1/cloud","af1/download","ag3/ag3.0","ag3/ag3.1","ag3/ag3.10","ag3/ag3.2","ag3/ag3.3","ag3/ag3.4","ag3/ag3.5","ag3/ag3.6","ag3/ag3.7","ag3/ag3.8","ag3/ag3.9","ag3/analysis","ag3/api","ag3/cloud","ag3/download","ag3/methods","amin1/api","amin1/cloud","amin1/download","amin1/intro","landing-page","release-notes","studies-ag1000g","vobs/vobs-data-access"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":5,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,"sphinxcontrib.bibtex":9,sphinx:56},filenames:["af1/af1.0.ipynb","af1/af1.1.ipynb","af1/af1.2.ipynb","af1/af1.3.ipynb","af1/api.md","af1/cloud.ipynb","af1/download.ipynb","ag3/ag3.0.ipynb","ag3/ag3.1.ipynb","ag3/ag3.10.ipynb","ag3/ag3.2.ipynb","ag3/ag3.3.ipynb","ag3/ag3.4.ipynb","ag3/ag3.5.ipynb","ag3/ag3.6.ipynb","ag3/ag3.7.ipynb","ag3/ag3.8.ipynb","ag3/ag3.9.ipynb","ag3/analysis.ipynb","ag3/api.md","ag3/cloud.ipynb","ag3/download.ipynb","ag3/methods.md","amin1/api.md","amin1/cloud.ipynb","amin1/download.ipynb","amin1/intro.ipynb","landing-page.md","release-notes.md","studies-ag1000g.md","vobs/vobs-data-access.ipynb"],objects:{},objnames:{},objtypes:{},terms:{"0":[1,5,6,8,9,10,11,12,13,14,15,16,17,20,21,22,27,28,29,30],"00":[5,20,24,29],"000":[22,24],"0000":20,"00000":[5,20],"000000":20,"00000100000":[5,20],"000001651491700000":20,"000001651491800000":20,"00000200000":[5,20],"000002063385700000":5,"000002063385801101":5,"00001":22,"0007664303506418854":21,"00101":5,"0011500862564692352":21,"0013417672992141077":21,"0015322735108216816":21,"0017244682889442423":21,"001915341888527102":21,"002106069308826345":21,"0024904214559386974":21,"00258":[24,25],"00264":[24,25],"0028":29,"0028735632183908046":21,"0035":29,"00384":[24,25],"00393":29,"006":22,"00611":29,"007":24,"008":29,"009":[5,6,24],"01":[5,21,22,29],"010":[5,20,24],"01055":29,"012":[22,24],"01230604":24,"01234":[5,20,24],"0125":20,"012500":20,"014":29,"014316392269148175":21,"01454":24,"01465":24,"01499":24,"01591":24,"016":29,"01604":24,"016488046166529265":21,"0165149170":20,"0165149180":20,"0167":29,"017":29,"018868":20,"019":29,"01949":24,"02":29,"020":[5,20,24],"0206338570":5,"0206338580":5,"022857025604":24,"022857026604":24,"023":24,"023571428571428573":21,"025":[24,26],"026":29,"02604":24,"02631578947368421":21,"027":24,"028":24,"02960":[24,25],"02986":29,"03":[20,25,29],"030928":20,"032":24,"033":[24,29],"0375":20,"037500":20,"03873":25,"04":[21,25],"04070":[24,25],"041":24,"04121":25,"041237":20,"049":29,"05":[20,29],"050":29,"05011":25,"051":24,"05167":25,"055":29,"057":24,"06":[20,25,29],"061":24,"062":24,"0625":20,"06692864":20,"06693":20,"068":24,"0680161":29,"06931525":20,"07":[20,25,29],"076923":20,"07_gamb_2004":20,"08":20,"080":29,"081":[7,22,28],"083":[5,6],"08729639":20,"09":[20,21,29],"093443":29,"094":29,"099":24,"09_colu_2012":20,"09_colu_2014":20,"09_gamb_2012":20,"09_gamb_2014":20,"0_funestus_":6,"0_funestus_3rl_phas":6,"0g":21,"1":[3,5,6,7,9,10,11,12,13,14,15,16,17,20,21,22,24,26,27,28],"10":[0,5,6,7,17,20,21,22,24,26,27,29],"100":[5,6,7,20,21,22,24,29],"1000":[7,18,20,21,22],"10000":5,"1000000":[6,21],"1002":11,"1004236":29,"1009253":29,"101":[7,16,20,21,29],"1015":6,"1016":29,"102":[7,20,21,24,26],"102870901":5,"102872101":5,"102872400":5,"102873600":5,"102882608":5,"102882609":5,"102882610":5,"102882611":5,"102882611allel":5,"102882901":5,"102883200":5,"102883201":5,"102883500":5,"102883501":5,"102883511":5,"103":[20,24,29],"10362":29,"1038":29,"103mb":5,"104":[12,20,24,25,26],"1046":29,"105":[20,24],"10506474":20,"1051":20,"10583542":29,"106":[24,26],"107":[24,26],"109":29,"1093":29,"1095":12,"10g":21,"11":[5,11,17,20,21,24,25,26,29],"110":[2,20],"1101":[26,29],"1106":5,"111":[20,29],"1111":29,"112":[20,29],"1121":29,"11226723":20,"1125":20,"1126":29,"113":[14,17,20],"113208":20,"11354":29,"1138":[1,10],"114":5,"1140":13,"1150":1,"116":24,"1164":9,"11646":29,"117":16,"1175":25,"1177":[8,10],"1178":[1,11],"1186":29,"1188":9,"119":[5,29],"1190":[1,11,15],"1191":[1,12],"12":[2,5,8,14,16,17,20,21,22,24,25,26,29],"120":[20,24],"1200":22,"1203":29,"12084":29,"121":11,"122":[17,24],"1221":29,"1229":[0,5,6],"122kb":5,"123":20,"1230":[0,1,5,6,16],"1231":[0,5,6,29],"1232":[0,5,6],"1235":[0,5,6],"1236":[0,1,2,3,5,6],"1237":[1,10,15],"1240":[0,5,6],"1242":29,"1244":[1,10,12],"1245":10,"1246":15,"125":[5,20,24,29],"12510902":29,"1253":10,"126":20,"1261":29,"1264":[1,13],"127":20,"1270":[9,13,15,17],"1272":13,"1273":[1,14],"1274":[17,29],"1275":29,"1279":14,"128":20,"1280":[14,17],"1281":[2,15,17],"1288":[1,14,16],"129":20,"12950":20,"13":[0,5,7,15,20,21,22,24,25,26,29],"130":[22,24,29],"1303":29,"13071308130913101311000000":5,"131":16,"1312":5,"1314":16,"1315":[1,16],"1323":17,"13245149":20,"1325":20,"1325arrai":20,"1326":[1,16],"1329":17,"133":[24,29],"1330":9,"1332939":20,"1333":20,"134":[14,20],"1349":29,"135":20,"135gb":5,"136":24,"1365":29,"137":7,"1371":29,"13754":20,"138":3,"14":[5,12,20,24,29],"140":29,"1404":14,"141":[12,20,24],"1415":24,"142":10,"143":29,"144":[17,20,24],"145":13,"146":17,"1470":20,"1470variant":20,"1472":29,"1475":29,"148718":29,"149":[9,29],"15":[5,7,12,16,17,20,22,24,26,29],"150":[22,24,29],"1500":20,"151":21,"15149":20,"153":[16,20,24],"1534":29,"154":20,"155":[24,26],"156":29,"157":13,"158":[5,14],"159":24,"159160161162163000000":20,"15x10x5cm":29,"16":[5,8,9,11,15,16,20,22,24,29],"160":[13,20,29],"161":29,"162":20,"163":[11,14,17,20],"1630":17,"164":[9,12,20],"16420701":29,"165":[13,20],"165149160":20,"1651491600000":20,"16514919":20,"16514919coordin":20,"166":[8,14,17,20],"167":[5,12,20],"168":[20,24,29],"16896122":29,"169":[20,29],"17":[5,6,9,16,20,21,29],"170":20,"171":[20,24],"17177993":29,"172":[7,20,24],"173":[9,15,20],"1736":20,"174":[7,20,21],"175":[20,29],"1756":29,"175mb":5,"176":20,"177":2,"178":[14,24],"179":[10,16],"17th":[8,10,11,12,13,14,15,16],"18":[0,1,5,16,17,20,24,29],"180":[9,29],"181":[7,11,20,21],"1817":12,"18187801":29,"182":[14,29],"183":[12,29],"184":20,"18496":20,"185":[7,20,21],"186":11,"188":17,"189":20,"19":[1,5,7,13,16,17,20,22,28,29],"190":[16,20],"192":20,"193":[3,20,21,29],"19303125":29,"194":20,"195":20,"19579":20,"196":20,"1968":29,"197":[5,11,24],"1979":29,"19797":20,"1986":9,"1987":29,"1988":9,"199":20,"1993":[7,29],"1994":7,"1997":29,"1998":[17,29],"1999":29,"1arrai":20,"1gb":5,"1mb":5,"1s":5,"1sa":29,"1tb":5,"2":[1,5,7,11,12,15,16,17,20,22,24,25,27,28],"20":[5,13,14,20,22,24,29],"200":[20,21,22,29],"2000":[2,7,22,29],"2001":[1,2,13],"2002":[2,7,17,29],"2003":[7,17,29],"2004":[1,7,9,17,29],"2005":[1,7,9,17,29],"2006":[1,7,17,29],"2007":[1,7,15,17,29],"2008":[1,9,15,16,29],"2009":[7,9,17,20,29],"201":[14,20],"2010":[1,7,9,17,24,26,29],"2011":[1,7,16,17,22,24,26,29],"2012":[1,7,8,9,15,16,17,20,21,22,29],"2013":[1,7,8,10,11,13,16,17,29],"2014":[0,1,7,8,10,12,13,15,16,17,24,26,29],"2015":[0,1,5,7,8,9,10,12,16,17,22,24,26,29],"2016":[0,1,11,12,13,15,16,22,24,25,26,29],"2017":[0,1,5,6,9,10,11,12,13,14,16,17,22,29],"2018":[0,1,10,11,12,13,14,15,16,17],"2019":[1,13,14,15,16,17,22,25,29],"202":[20,24],"2020":[1,2,9,13,14,15,16,17,29],"2021":[1,9,14,15,16,17,26,29],"20211101":[20,28],"2022":[1,2,3,9,17,21],"2023":[2,3],"20231215":5,"2025":[8,10,11,12,13,14,15,16],"2026":[0,1,2,3,9,17],"203":[20,21],"204":11,"205":20,"205151":20,"205151coordin":20,"206":20,"206338560":5,"2063385600000":5,"20633859":5,"20633859allel":5,"207":7,"208":[16,20],"209":[20,24],"20c":29,"21":[1,5,9,15,17,20,24,29],"210":29,"2100":20,"2104":[1,16],"212":[17,24],"2125":29,"213":[20,24],"2132":29,"214":1,"215":24,"216":20,"217":29,"21866":20,"219":[20,29],"21mb":5,"22":[0,1,5,7,20,24,29],"2203":[1,16],"2204":16,"2208":29,"221":[20,24],"221variant":20,"222":[20,29],"223":17,"224":20,"225":[20,29],"226":20,"2261":16,"227":[15,20],"228":[20,24],"22857024604":24,"22857027":24,"23":[5,7,8,10,20,21,29],"2304":9,"233":[21,29],"234":[20,24],"235":[11,20,21,29],"236":20,"237":12,"239":[5,20],"24":[5,11,15,16,17,20,22,24,29],"240":[20,24],"24061":29,"243":[16,20],"244":20,"245kb":5,"246":[15,24,29],"24th":9,"25":[5,15,20,24,29],"250":22,"251":5,"252":[9,20,21,24],"252k":21,"253":20,"2546":15,"255":15,"256":[5,20],"257":24,"258551":21,"259":[20,24],"25928":20,"25h":[20,24],"25hdone":[20,24],"25l":[20,24],"26":[5,7,11,16,20,24,26,29],"260":24,"261":29,"262":20,"262144":[5,20],"263":1,"265":[11,17],"268":[10,15],"27":[1,5,7,20,29],"270gb":5,"271":[20,24],"272":29,"273":[15,17,24],"2738":29,"274":[20,29],"2749":29,"276":[15,29],"2779278027812782278300":20,"2784":20,"2784variant":20,"27gb":5,"28":[1,5,7,9,11,12,17,20,21,29],"281":5,"283":[8,29],"28465673":20,"28472728":20,"28473600":20,"28473874":20,"28474576":20,"28475128":20,"28475490":20,"28475996":20,"28477220":20,"28477540":20,"28477710":20,"28477889":20,"28478057":20,"28478272":20,"28478925":20,"28478987":20,"28479181":20,"28479407":20,"28479548":20,"28480166":20,"28480189":20,"28480193":20,"28480335":20,"28480372":20,"28480547":20,"28480585":20,"28483069":20,"28483236":20,"28483253":20,"28483372":20,"28483384":20,"28483442":20,"28483473":20,"28483475":20,"28483675":20,"28484157":20,"28484338":20,"28484518":20,"28485005":20,"28485033":20,"28485380":20,"28486036":20,"28487546":20,"28491215":20,"28491431":20,"28493547":20,"28494017":20,"28494597":20,"28496505":20,"28496700":20,"28496953":20,"28497279":20,"28497740":20,"28499200":20,"28518123":20,"28520016":20,"28522671":20,"28555300":20,"28556726":20,"28563596":20,"287":14,"2875":29,"28795255":20,"288":[5,29],"288b":5,"289":20,"29":[1,5,20,24,29],"290":[7,20,21],"291":29,"2915":29,"292":[5,24],"293":29,"294":[20,24],"295":20,"297":[7,20,21,22,24],"29729829930030100":24,"298":[20,24],"299":[20,24,29],"29th":[0,1,2,3],"2arrai":20,"2c":29,"2coordin":5,"2gb":5,"2kb":5,"2l":[20,21],"2min":20,"2ploidi":20,"2r":[20,21],"2rb":29,"2rj":29,"2rl":[5,6],"2rl_sitefilt":6,"2sampl":[5,20,24],"3":[1,2,5,6,9,12,15,17,20,21,22,24,25,27,28],"30":[5,20,22,24,29],"300":[5,6,7,20,21,22,24],"300000":[5,20,24],"301":[5,20,24],"30141517":24,"301415170008301415186000301415194000":24,"30141518":24,"30141519":24,"30141520":24,"30141520coordin":24,"302":[20,24,26],"302variant":24,"303":[7,20,21],"305":[6,17],"306":24,"30614":5,"30614sampl":5,"3076":20,"3076307730783079308000":20,"3077":20,"3078":20,"3079":20,"3080":20,"3081":20,"3081coordin":20,"3081variant":20,"30km":29,"31":[0,5,7,9,20,21,24,29],"313":[13,24],"3156":29,"31626230":24,"317":2,"31kb":5,"32":[5,7,9,17,20,24,29],"320":[0,5,6,20],"321":20,"3222999974":21,"323":16,"327":[15,16],"329":22,"33":[5,7,16,20,24,29],"3305":29,"334":5,"34":[0,5,24,29],"341":29,"3426":20,"342946":5,"342946sampl":5,"343":5,"3436926":20,"343kb":5,"344":1,"3447950":20,"345":29,"346":24,"34853":20,"35":[5,17,29],"350":29,"3501850":20,"3512200":20,"3518900":20,"3535850":20,"3539300":20,"356":24,"357":24,"3573750":20,"3599050":20,"36":[0,1,5,6,7,10,16,21,24,26,29],"360":29,"3616290":20,"3619":29,"3619000":20,"3639":17,"3639836":20,"364":24,"3654":20,"3668":20,"3668sampl":20,"367":29,"368":20,"36ploidi":5,"37":[0,12,13,20,24,29],"376":24,"379":14,"38":[5,10,17,20,22,24,29],"380":[15,20],"382":13,"384":29,"388":24,"38878":20,"39":[1,5,20,24,26,29],"392":5,"394":5,"394408":29,"395":24,"398":10,"3af":29,"3arrai":20,"3l":[20,21,22],"3r":[5,6,20,21,22],"3r_sitefilt":21,"3rl":[5,6],"3sz":29,"4":[1,5,6,7,9,11,13,15,17,20,21,22,24,25,26,27,29],"40":[0,5,6,20,24,26,29],"400":29,"408":29,"409":20,"40coordin":20,"41":[0,7,16,17,20,21,24,29],"410":29,"411":24,"412mb":5,"413":24,"414":24,"417":29,"41mb":5,"42":[5,9,20,29],"420":[5,6],"421":24,"422":12,"423":29,"4248stdy7308980":[24,25],"4248stdy7308981":[24,25],"4248stdy7308982":[24,25],"4248stdy7308986":[24,25],"4248stdy7308989":[24,25],"4248stdy7308990":25,"4248stdy7308994":25,"4248stdy7308996":25,"4248stdy7308997":25,"4248stdy7918667":24,"4248stdy7918668":24,"4248stdy7918669":24,"4248stdy7918670":24,"4248stdy7918671":24,"4269":29,"428":24,"43":[0,1,5,6,16,29],"437":24,"439":24,"44":[0,5,7,20,21,24,29],"442":29,"443":21,"45":[0,5,7,17,20,21,24,29],"450":[24,29],"451":15,"452":24,"453":[1,21,24],"455":29,"46":[7,16,20,24],"461":[24,29],"4625":20,"464":[24,29],"46556":29,"467":15,"468":15,"468219":26,"469":29,"47":[5,20,24,26,29],"472":[21,24,29],"476":24,"477":29,"4779799":5,"47803":20,"479":24,"48":[9,29],"480":24,"482":24,"483":[14,29],"484":24,"485":12,"488":[5,6],"49":[0,11,17,29],"494":24,"497":[5,6,29],"49k":21,"4kb":5,"4km":29,"4min":24,"4ploidi":[20,24],"4s":20,"4sampl":5,"5":[5,6,7,8,9,11,14,15,17,20,21,22,24,26,27,29],"50":[0,1,5,6,15,20,21,22,24],"500":29,"501":24,"502":[5,20],"506":29,"507":20,"508":13,"51":[5,8,20],"511":[5,29],"511b":5,"511coordin":5,"512":5,"514":20,"516":29,"52":[15,20,29],"520":[24,29],"52226565":20,"52226566":20,"52226567":20,"52226568":20,"52226568coordin":20,"524":[20,24],"524288":[5,20,24],"529":[24,29],"53":[7,16,20,21,29],"532":20,"53226":29,"533":22,"534":24,"535":29,"536":24,"537":24,"54":[7,13,24],"540gb":5,"544":24,"545":29,"548":[24,26],"5488":5,"549":29,"55":[1,2,3,20,24,29],"550":29,"552":17,"554":24,"55635564556555665567000000":20,"5568":20,"558":29,"56":[20,29],"563":22,"564":17,"565":22,"566038":20,"567":29,"569":24,"57":[5,11,12,20,24],"571":24,"578":24,"58":[17,24],"582":29,"583":29,"586":24,"59":[2,5,16,17,24],"594":[5,24],"595":[24,26],"5kb":5,"5m":[21,29],"5ml":29,"5s":24,"6":[1,5,7,9,10,13,15,16,17,20,21,22,24,25,27,29],"60":[7,13,20,21,24],"600":[5,20],"601":[5,20],"602":[1,24],"604":[24,29],"605":20,"609":29,"61":[5,20,21],"61303692":20,"61306248":20,"61372543":20,"614":20,"61418536":20,"61478226":20,"61478226arrai":20,"61478802":20,"61478802arrai":20,"61514401":20,"61515901":20,"61517400":20,"61517700":20,"61533301":20,"61535700":20,"615385":20,"61544401":20,"61544700":20,"61544701":20,"61545000":20,"61545001":20,"61545105":20,"617":29,"618557":20,"62":[5,9,21],"624":24,"627":24,"629":29,"62mb":21,"63":[12,16,20,21,22,24],"632":20,"633":5,"634050":29,"639":24,"64":[5,7,10,20,29],"641":24,"642":29,"646":24,"647":[8,24],"649":29,"64b":5,"65":[7,12,17,20],"650":29,"651":5,"6516526536546550":5,"65165265365465500":5,"652":5,"653":5,"654":5,"655":[5,24],"65536":[5,20],"656":[0,5,20,29],"656ploidi":5,"659":24,"66":[20,24,26],"660":[9,24],"663":24,"666":10,"667":[24,25,26,29],"668":[5,29],"669":7,"67":[20,24],"674":24,"6768697071000000":5,"678":24,"6785":29,"67gb":5,"68":[5,7,29],"680":29,"683":17,"685":24,"6885930":29,"689":24,"69":[7,12,14,15,20,21,24],"690":29,"693":22,"6am":29,"6pm":29,"7":[1,5,6,7,10,11,16,20,21,22,24,27,29],"70":[16,20,24,29],"700":29,"701":29,"701mb":5,"703":24,"707":24,"708":24,"71":[5,7,20,21,24],"710":24,"711":24,"716":29,"717391":20,"719":24,"72":[5,9,17,24],"721":29,"722":24,"725":24,"726":[24,29],"73":[7,8,20,21,24,29],"730":24,"733":24,"7335":20,"735":[24,26],"737":24,"739":16,"74":[7,11,20,21,24],"741":24,"742":[24,29],"743":24,"744":24,"746":24,"747":29,"7475":29,"75":[9,20,24,29],"750":29,"75015":29,"751":29,"7524":20,"755":29,"757":24,"76":[0,5,6,7,11,14,20,21,24],"762":[24,29],"77":[13,20,24,26,29],"774":29,"776":24,"777":29,"779":29,"78":[5,10,20,21,24,29],"784":[7,20,22],"79":[5,29],"79113":5,"79116":5,"79117":5,"79120":5,"79128":5,"79129":5,"79130":5,"79133":5,"79134":5,"79136":5,"792":24,"7ht":29,"7py":29,"8":[0,1,5,6,7,9,15,17,20,21,22,24,27,29],"80":[7,20,21,24,29],"800":[24,29],"80101":5,"80108":29,"803":24,"81":[0,2,5,6,7,20,21,29],"810":29,"817":29,"82":[7,20,24],"820":20,"821":29,"822":24,"82200":5,"823":[24,29],"825":24,"82variant":20,"83":[20,24,29],"83400":5,"83401":5,"838":24,"83mb":5,"84":[5,7,20],"840":29,"843":24,"844":29,"849":[24,29],"85":[5,13,15,20,24],"851":5,"855":24,"8567335243553008":21,"857":24,"859":5,"86":[5,7,20,21,24],"860":29,"861":29,"864":24,"86400":5,"8658536585365854":21,"868":29,"8686288585786073":21,"87":[7,20,24],"870":29,"870157819225251":21,"873":24,"875":24,"88":[5,12,20,24],"880":29,"884":20,"89":[20,29],"890":29,"891":29,"8925":20,"897":24,"898":[24,29],"8coordin":5,"9":[1,5,6,7,9,10,12,15,16,20,22,24,26,27,29,30],"90":[5,7,10,12,20,22,24,29],"900":[5,20,29],"90036":29,"91":[5,20],"910":24,"912":29,"913":[24,29],"9157060518731989":21,"916":24,"917":29,"918":24,"919":20,"91m":21,"92":[5,14,20,24,26],"9203":29,"922":24,"9247311827956989":21,"928":24,"93":[7,20],"933":29,"938":24,"94":[1,9,12,14,16,20,24],"94080":29,"941":24,"941923":24,"943":24,"9459":20,"9459coordin":20,"94kb":5,"95":[1,15,20,22,29],"952":[5,6],"957":29,"96":[9,20],"966":24,"969":20,"97":[5,7,15,20,21,29],"972":29,"972083035075161":21,"9735973597359736":21,"974":24,"975":16,"9750830564784053":21,"977":24,"9777411376751854":21,"979":20,"98":[5,20],"9801652892561984":21,"9810074318744839":21,"982":[24,25,26],"984297520661157":21,"9875930521091811":21,"99":[5,7,17,20],"991":29,"995":[24,26],"995f":29,"996":24,"9985":20,"9th":17,"\u00e0":29,"\u00e8":29,"\u00e9":29,"amab\u00e9lia":29,"boolean":[5,20,24],"byte":[5,20,24],"case":[1,2,3,5,6,21,29],"catch":29,"class":[5,20,22,24],"default":[5,6,30],"diabat\u00e9":29,"direc\u00e7\u00e3o":29,"djogb\u00e9nou":29,"do":[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,29,30],"end\u00e9mi":29,"final":[22,29],"float":29,"fr\u00e9d\u00e9ric":29,"function":[4,5,6,19,20,22,23],"guina\u00e9":29,"import":[5,20,24],"jo\u00e3o":29,"k\u00e9toh":29,"long":[5,20,21],"m\u00fcller":29,"mal\u00e1ria":29,"mich\u00e8l":29,"minist\u00e9rio":29,"minista\u00e9rio":29,"new":[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26,28,29,30],"null":22,"p\u00e5lsson":29,"p\u00fablica":29,"pa\u00fablica":29,"pag\u00e8":29,"public":[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26,30],"regi\u00e3o":29,"resist\u00eancia":29,"return":[5,20],"ros\u00e1rio":29,"s\u00e6b\u00f8":29,"sa\u00fad":29,"saa\u00fad":29,"sangar\u00e9":29,"sant\u00e9":29,"short":[0,7,29],"static":[5,6],"tiassal\u00e9":29,"true":[1,2,3,5,20,22,24,29],"universit\u00e0":29,"while":29,"yaound\u00e9":29,A:[5,6,7,20,21,22,24,25,28,29],As:[5,20],At:29,For:[1,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,29],IN:29,If:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,28,30],In:[0,5,7,20,29],It:29,No:[22,24],Not:[5,20,22,24],On:[5,20],One:22,The:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,26,28,30],Then:[6,21],There:[5,6,20,21,29],These:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29,30],To:[1,2,3,5,6,18,20,21,22,24,25,27,30],With:29,_:21,_funestus_:6,_phase:[6,21],ab0085:21,ab0086:21,ab0087:21,ab0088:21,ab0089:21,ab0090:21,ab0091:21,ab0092:21,ab0094:21,abaga:29,abdisalan:29,abdoul:29,abdoulay:29,abdrahaman:29,abidjan:29,abl:[5,20,22],about:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,29],abov:[0,1,2,3,5,9,10,11,12,13,14,15,16,17,20,21,22,25],abrahan:29,absenc:[5,20,29],absolut:29,abyzov:22,ac0398:29,ac:[0,5,6,20,21,24,25,29],ac_pass:24,academ:30,acc:20,access:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,27],accommod:22,accord:[22,29],account:22,accra:29,ace1:[20,22,29],ace1_del1:20,ace1_del2:20,ace1_del3:20,ace1_del4:20,ace1_dup0:20,ace1_dup1:20,ace1_dup2:20,acet:29,acetylcholin:20,acetylcholinesteras:29,acid:[20,29],acoust:22,across:[0,5,6,17,20,21,22,29,30],activ:29,actual:[5,20,24],ad0494:20,ad0495:20,ad0496:20,ad0497:20,ad0498:20,ad:[1,2,3,5,6,21,22,28,29],adam:29,adapt:[1,2,3,5,8,9,10,11,12,13,14,15,16,17,20,22,29],add:[5,6,20,21,24,25],addit:[7,29],addition:21,address:30,adher:30,adiamoh:29,admin1_iso:[5,20],admin1_nam:[5,20],admin1_year:20,admin2_nam:[5,20],adok:29,adopt:[1,2,3,8,9,10,11,12,13,14,15,16,17],adult:29,advis:30,aerosol:29,aestiv:[8,10],af1:27,af1_sc:5,af:[1,6],affect:22,africa:[0,1,9,14,16,17,29],african:[0,1,7,10,12,13,15,17,18,28],afriqu:29,afrotrop:29,after:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26,29],ag1000g:[1,18,20,21,22,27],ag3:[1,27,28],ag3_:21,ag3_gamb_colu_arab_3l_phas:21,ag:21,agamp4:22,agap001096:20,agap001097:20,agap001098:20,agap004674:20,agap004675:20,agap004676:20,agap013094:20,aggfunc:24,ago:20,agreement:30,agricultur:29,ah32:6,ai:30,aim:[20,21],aim_20200422:20,aim_speci:[20,21],aim_species_fraction_arab:21,aim_species_fraction_colu:21,aim_species_fraction_colu_no2l:21,aim_species_gambcolu_arabiensi:21,aim_species_gambiae_coluzzii:21,ajtmh:29,akron:29,al:[22,26,29],alcohol:29,alert:29,alessandra:29,alessandro:29,alexand:29,alexandra:29,ali:29,align:[0,5,6,7,20,24,26],alignments_bam:25,alina:29,alinun:29,aliv:29,all:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,29,30],allel:29,allele_consist:21,allelecountsarrai:24,allelism_count:24,alli:29,allison:29,alloc:30,allow:[0,5,6,20,21,22,24,30],almost:29,along:[22,29],alpha:22,alphabet:7,alreadi:[21,25],also:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29],alt:[6,21],altern:[5,6,20,21,22,24,25,30],although:[1,2,3,5,8,9,10,11,12,13,14,15,16,17,20,29],alwai:[5,6,20,21,24],am:29,amabelia:29,amad:29,ambigu:22,ambros:29,amenga:[1,11,15],american:29,amfaal:29,amharicu:29,amin1:[27,28],among:[22,29],amount:21,amp:20,amplic:22,amplif:[5,20],amplifi:22,an:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,28,29,30],analys:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,24,25,26,28,29],analysi:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,25,26,27,28,29],anatol:29,ancestri:21,angela:29,angola:[7,17,20],ani:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,28,29,30],anim:29,anitha:29,ann:29,annot:[20,22],annual:29,anophel:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,26,28,29],anophelin:29,anophelina:29,anospp:[0,1,16,17],anoth:30,antananarivo:29,antao:29,antula:29,ao:[7,20,21,29],ao_:21,ao_cnv_discordant_read_cal:21,ao_cnv_hmm:21,ao_gamb_colu_2l_phas:21,ao_gamb_colu_cnv_coverage_cal:21,api:[5,18,20,27],appar:[22,29],appear:29,appendix:22,appli:[5,20,21,22,24],applic:[21,30],approach:[1,2,3,8,9,10,11,12,13,14,15,16,17,22],appropri:[1,2,3,8,9,10,11,12,13,14,15,16,17,22],approxim:[5,6,20,21,22,24,25,29],apr:[24,25],april:[0,1,2,3,17,29],ar0001:[20,21],ar0002:[20,21],ar0004:[20,21],ar0006:[20,21],ar0007:[20,21],ar0008:21,ar0009:21,ar0010:21,ar0011:21,ar0047:[20,21],ar0049:[20,21],ar0051:[20,21],ar0061:[20,21],ar0072:21,ar0078:[20,21],ar0080:21,ar0084:21,ar0097:21,ar:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,26,29],arab:[20,21,22],arabiensi:[7,8,9,10,11,12,13,14,15,16,17,20,21,28,29],archiv:[0,6,7,21],area:[22,29],arez:29,arid:29,arj:29,arlet:29,arm:[5,6,20,21,22],around:[6,21,22,29],arrai:[5,20,24],articl:29,ascertain:29,asciitre:[20,24],ascot:29,asia:26,ask:30,aspir:29,assai:29,assess:[17,29],assign:[20,21,24,25,29],associ:[6,17,21,22,25,29,30],assum:[5,6,20,21,24,25],attribut:[5,20,24],august:29,aurelio:29,auroc:22,austin:[21,29],auth:30,authent:[5,6,20,21,24,25],automat:30,autosom:[5,20,22,29],avail:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,28,30],avaradoha:29,averag:22,avoid:22,awai:29,await:21,awolola:29,axi:24,ayala:[0,1,5,6,16,29],aydi:[1,16],b5:29,b:[5,6,7,20,21,22,24,25,29],back:[5,20,22,24],badzer:29,bag:29,balanc:22,baltimor:29,bam:6,bamako:29,bana:[21,29],banambani:29,bancoumana:29,bangui:29,banjul:29,bank:29,bap:29,barri:29,barron:15,base:[5,6,15,20,21,22,24,25,29],baselin:0,basi:29,basiliana:29,bass:29,bcftool:[6,21],beavogui:29,becaus:[5,6,20,21,22,24,30],becki:29,been:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,24,26,28,29],befor:[0,1,2,3,8,9,10,11,12,13,14,15,16,17,22,29],being:22,bejon:29,belong:[6,20,21],below:[0,5,6,7,20,21,22,24,27,29],bendiocarb:29,beneath:22,benedict:29,benefit:30,beniamino:29,benin:[0,1,10,15,17,29],benjamin:29,bennett:29,berg:29,bergei:17,berkshir:29,besanski:29,best:[5,20,22,24,30],better:22,between:[5,8,17,20,22,29],bf2:21,bf3:21,bf:[7,16,20,21,29],bia:29,biallel:[5,20,21,22,24],bias:22,bika72:29,bilali:29,bincount:24,binomi:22,bio:29,bioassai:29,biol:29,biolog:[1,2,3,8,9,10,11,12,13,14,15,16,17,29],biologi:29,bionom:29,biorxiv:26,bioscienc:29,birom:29,bissau:[7,17,22],bite:29,bj:[1,10,15],bl0047:20,bl0048:20,bl0049:20,bl0050:20,bl0055:20,blacksburg:29,blantyr:29,block:22,blood:29,bloomsburi:29,bmc:29,board:[5,6,20,21,24],boas:29,bobo:29,bolognetti:29,bool:[5,20,24],booldask:[5,20,24],boolfals:20,border:29,borongo:29,bortel:29,both:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26,29,30],botha:29,boto:6,bott:29,boubacar:29,bov:29,box:29,bp:[5,6,20,21,22,29],bradlei:29,bradwhit:29,brama:29,brandi:[24,25,26],brandyc:26,breakdown:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,29],breakpoint:[5,6,20,21,22,29],breed:29,bretz:29,brian:29,briefli:22,broad:22,broader:22,brogdon:29,broken:7,brows:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26],browser:[21,29],bryan:29,bucket:[5,6,20,21,24,25],bug:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,24,26,28],build:[0,1,2,3,6,8,9,10,11,12,13,14,15,16,17,20,21,24],burkina:[2,7,9,12,15,16,20,21],burt:[21,29],buya:29,bwa:22,byaruhanga:29,c:[5,7,20,21,22,24,29],ca:29,cabo:5,caccon:29,cach:5,calcul:[5,20],calibr:22,california:29,call:[27,28],call_ad:[5,20,24],call_cn:[5,20],call_genotyp:[5,20,24],call_genotype_mask:[5,20,24],call_gq:[5,20,24],call_mq:[5,20,24],call_normcov:[5,20],call_rawcov:[5,20],calldata:[6,21],callset:21,calvin:29,calzetta:29,cambodia:[24,25,26,28],cambridg:29,came:[26,29],cameroon:[0,2,7,9,15,17],campo:[17,29],can:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,26,29,30],cani:29,cano:29,canon:29,cap:22,cape:29,capit:29,captur:29,caputo:29,carbam:29,carcass:29,carlo:29,carlsbad:29,carnoi:29,carolin:29,carrara:29,carri:[0,7,20,22,26,29],cat:[6,21],catalog:[6,21,25],catchment:29,caught:[7,20,21,22,29],cb10:29,cb:[24,25],cd:[0,1,5,6,7,13,20,21,29],cdc:29,cell:29,cenci:29,center:[26,29],centr:[22,29],central1:5,central:[0,1,7,16],centrifug:29,certain:[6,21],cf:[0,5,6,7,20,21,29],chabi:29,chain:[20,29],chamkar:[24,26],chang:[1,2,3,6,8,9,10,11,12,13,14,15,16,17,21,22,25],character:[2,15,22,29],characteris:29,charif:29,charl:29,charlwood:29,chean:[24,26],check:[29,30],cheick:29,chichiri:29,chickhwawa:29,chikhwawa:29,chipeta:29,chloroform:29,choi:29,choos:[5,20,22,24],chosen:[5,20,24],chri:29,christel:29,christian:29,christoph:[2,15,17,29],christophid:29,chromosom:[5,6,20,21,22,29],chunk:[5,20,24],chunksiz:[5,20,24],ci:[7,10,14,20,21,29],cincinnati:29,circumst:[1,2,3,8,9,10,11,12,13,14,15,16,17],cite:26,citi:[22,29],clarkson:29,classif:22,classifi:22,clear:[22,29],clement:29,cli:30,click:[5,20,24],client:5,climat:29,clinic:29,clobber:[6,21,25],closer:[5,20,24],cloud:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,21,25,26,27],cluster:[5,6,20,21,22,29],cm:[2,7,15,17,20,21,29],cn:[5,20,22],cn_mode:20,cn_mode_count:20,cnm:26,cnr:29,cnrfp:29,cnv:[1,2,3,8,9,10,11,12,13,14,15,16,17,28],cnv_coverage_cal:[5,20],cnv_discordant_read_cal:20,cnv_hmm:[5,20],cnv_type:20,co:29,coast:29,coastal:29,cocoa:29,code:[5,6,7,20,21,24,25],coetze:29,coffinet:29,cog:[6,21,25],cohort:[5,6,7,20,21,22,24,25,28],cohort_admin1_month:[5,20],cohort_admin1_quart:5,cohort_admin1_year:[5,20],cohort_admin2_month:[5,20],cohort_admin2_quart:5,cohort_admin2_year:[5,20],cohort_queri:[5,20],coil:30,colab:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,24,26,30],colinc:29,collabor:[0,5,6,7,8,20,21,26,29],collect:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,22,24,25,26,29],colleg:29,collin:29,column:[5,6,20,21,24,25,29],coluzzi:29,coluzzii:[7,8,9,10,11,12,14,15,16,17,20,21,28,29],com:[20,21,25,29],combani:29,combin:22,come:0,command:[6,21,25,30],commerci:29,common:29,commonli:29,commun:[1,2,3,8,9,10,11,12,13,14,15,16,17,18,20,29,30],comoro:17,comparison:22,compat:[6,21,25],complement:22,complementari:22,complet:[5,6,20,21,22,24,29],complex:[7,9,29],complic:22,compon:22,composit:22,comprehens:29,compress:24,compris:[22,26,29],comput:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,21,22,25,26,29,30],computation:22,conakri:29,concentr:22,concord:22,conda:24,condit:29,conduct:29,confid:22,config:[5,6,20,24],configur:30,confirm:22,congo:[0,1,7,13],connect:[17,21,29],conserv:22,consid:22,consist:[22,29],consortium:[0,7,29],constant:[10,22,29],construct:[20,21,22,29],contact:[0,5,20,30],contain:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,29],contemporari:29,content:[6,21,22],context:26,contig:[5,6,20,21,24],contigu:[5,6,20,21,22],continu:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26,30],contr:29,contrast:29,contribut:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,29],contributor:[5,6,20,21,24,25],control:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26,29],conveni:[5,6,7,20,21,24],convent:29,convert:[5,20],conwai:29,coordin:[5,7,20,24,26,29],cooseman:29,copi:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26,28],core:[5,20],correctli:30,correspond:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24],correspondingli:29,correwyn:29,cost:30,costa:29,costantini:29,cote:[7,10,14],cotteaux:29,could:[5,6,20,21,22,24,25,30],couldn:20,coulibali:29,council:29,count:[5,20,22],count_allel:[5,20,24],count_nonzero:[5,20,24],counti:29,countri:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,28,29],country_iso:20,coupl:29,cours:[7,18,29],covari:22,cover:[22,29],coverag:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26,29],coverage_cal:[6,21],cp:[6,21],craft:22,craig:29,crawford:15,creat:[5,6,20,21,22,24],cromb:29,cropland:29,cross:[7,20],crosses_stat:21,csv:[6,21,25],ctab:[26,29],cuamba:29,cultiv:29,cup:29,curat:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26],current:[7,30],curv:22,cut:[6,21,25],cutoff:[5,6,22],cx:21,cyhalothrin:29,cyp6:29,cyp6aa1:22,cyp6aa:20,cyp6aap_dup0:20,cyp6aap_dup10:20,cyp6aap_dup11:20,cyp6aap_dup12:20,cyp6aap_dup13:20,cyp6aap_dup14:20,cyp6aap_dup15:20,cyp6aap_dup16:20,cyp6aap_dup17:20,cyp6aap_dup18:20,cyp6aap_dup19:20,cyp6aap_dup1:20,cyp6aap_dup1a:20,cyp6aap_dup1b:20,cyp6aap_dup20:20,cyp6aap_dup21:20,cyp6aap_dup22:20,cyp6aap_dup23:20,cyp6aap_dup24:20,cyp6aap_dup25:20,cyp6aap_dup26:20,cyp6aap_dup27:20,cyp6aap_dup28:20,cyp6aap_dup29:20,cyp6aap_dup2:20,cyp6aap_dup30:20,cyp6aap_dup3:20,cyp6aap_dup4:20,cyp6aap_dup5:20,cyp6aap_dup6:20,cyp6aap_dup7:20,cyp6aap_dup8:20,cyp6aap_dup9:20,cyp6m2:22,cyp6m4:22,cyp6p2:22,cyp6p:20,cyp6z1:22,cyp6z3:22,cyp9k1:22,cytogenet:29,d:[6,7,10,14,21,25],da:[5,20,24,26,29],dadzi:[0,5,6,29],dai:29,daiguen:29,daili:29,damari:29,dame:29,damox:20,danica:29,daniel:29,dar:29,dask:[5,20,24],data:[4,18,19,22,23,28,29],datafram:[5,20,24],dataset:[5,20,21,22,24,26],datasetdimens:[5,20,24],date:[1,2,3,5,6,20,21,24,25],dave:29,davi:29,david:29,dayanandan:29,daytim:29,ddt:29,de:[22,29],dead:29,decemb:29,decidu:29,decis:[5,6,22],declin:29,deco:29,deep:29,defin:[5,20],degrad:29,del:20,delet:[5,20,28,30],delgado:5,delimit:[6,21],della:29,dellatorr:29,deltamethrin:29,democrat:[0,1,7,13],den:29,deni:29,dens:29,dentistri:29,deokari:29,depart:29,depend:[0,5,6,7,20,21],deposit:29,depth:[18,20,22],deriv:[5,6,20,21,22],describ:[7,22,29],descript:22,desicc:29,design:[20,21,22],desir:29,despit:17,dessic:26,detail:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,21,22,28,29,30],detect:[1,2,3,8,9,10,11,12,13,14,15,16,17,29,30],determin:[5,6,20,21,22,24,29],develop:[18,22,29],df_gene_cnv_freq:20,df_sampl:[5,20,24],df_sample_set:[5,20],df_samples_phas:[5,20],df_summari:24,di:29,dia:29,diabat:29,diagnost:[1,5,10,12,15,20,22,24,29],diann:29,diatta:29,did:[22,29],didier:29,diego:29,dieldrin:29,differ:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,25,29],differenti:[21,29],diggl:29,dim:24,dimabi:[5,6],dimens:[5,20,24],dimension:[5,20,24],dimitra:29,dini:29,dioulasso:29,dip:29,dipartimento:29,diploid:[5,20,22],direct:[21,29],directli:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,29],directori:[6,21,25],disabl:6,disconnect:30,discord:28,discordant_read_cal:21,discuss:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26],diseas:[1,2,3,8,9,10,11,12,13,14,15,16,17,29],disk:21,displai:22,dissect:29,distanc:22,distinct:[26,29],distribut:[22,29],district:[1,11,15,29],diverg:26,divers:[0,1,11,13,14,15,17,26,29],divid:22,djibril:29,djogben:[1,10,15],dna:[5,7,20,22,26,29],dnaeasi:29,dnazol:29,dneasi:29,doc:[4,5,19,20,23],document:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,23,24,25,26,30],doe:29,doi:[26,29],domin:29,don:29,done:[6,29],donnelli:[1,14,16,20,29],doreen:29,dorsei:29,douala:29,doubt:29,doumbia:29,douna:29,down:[7,22],download:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,24,26,27,28],dr:0,drakelei:29,drc:29,dri:29,drive:[17,29],druri:29,dry:[24,25,29],ds_cnv:[5,20],ds_cnv_dr:20,ds_gene_cnv:20,ds_hap:[5,20],ds_haps_cohort:[5,20],ds_hmm:[5,20],ds_snp:[5,20,24],ds_snps_funestu:5,ds_snps_gambia:20,dt_20200416:[5,6,20,21],dtype:[5,20,24],due:[5,20,22],dup0:20,duplic:[22,29],dure:[1,2,3,8,9,10,11,12,13,14,15,16,17,22,29],durham:29,dwell:29,dynam:29,e1004236:29,e1009253:29,e:[5,6,7,20,21,22,24,29,30],each:[0,1,2,3,5,6,7,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29,30],earli:[24,25,29],easi:[21,29],easili:[6,21],east:[22,29],eastern:29,ebi:21,eck:29,eclos:29,eco:[2,15,29],ecol:29,ecolog:[1,11,15,29],edi:29,edit:[6,29],edu:29,educ:30,edward:29,effect:29,effici:[5,6,20,21,30],effort:29,egg:29,egyir:29,eight:29,either:[6,20,21,22,26],elev:[5,6,20,21],elien:29,elig:22,elisa:29,elissa:29,elong:20,em:29,email:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,30],embargo:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,30],emerg:[1,2,3,8,9,10,11,12,13,14,15,16,17,29],emerson:29,emidi:29,emili:29,emiss:22,empir:22,employ:30,emrich:29,en:29,ena:[0,6,7,21],ena_align:21,ena_analysi:21,ena_run:21,end:[5,20,22],endem:[1,2,3,7,8,9,10,11,12,13,14,15,16,17,29],engin:[17,22],enhanc:0,ensur:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,26],enter:22,entomol:29,entomolog:[26,29],environ:29,environment:[17,29],enzym:29,epidem:[1,2,3,8,9,10,11,12,13,14,15,16,17,29],epidemiolog:[2,13,15,27],epopa:29,eppendorf:29,equal:22,equatori:[7,17,29],eric:29,err323844:21,err328585:21,err328597:21,err343468:21,err343636:21,err343648:21,err347035:21,err347047:21,err352136:21,errat:22,error:[22,29],erz1695275:21,erz1695276:21,erz1695277:21,erz1695278:21,erz1695279:21,erz1695280:21,erz1695281:21,erz1695282:21,erz1695283:21,es:29,essandoh:29,establish:[1,2,3,8,9,10,11,12,13,14,15,16,17,29],estim:[22,29],et:[22,26,29],eta:21,etc:22,etego:[1,11,15],ethanol:29,ethic:[1,2,3,8,9,10,11,12,13,14,15,16,17],ethiopia:[9,13,17],ethiopian:29,etouna:29,european:[0,6,7,21],ev:29,eval:[5,20,24],evalu:[0,14,15,16,22],even:[6,22],event:22,evergreen:29,everi:[5,20,29],everyon:30,evid:22,evol:29,evolut:7,examin:22,exampl:[6,18,21,25,29],except:[20,22],excess:30,exclam:[6,21,25],exclud:[5,6,20,21,22,24],expect:[0,22],experi:6,experiment:[5,20,24],expertis:0,expir:[0,1,2,3,8,9,10,11,12,13,14,15,16,17],expiri:0,explor:[5,6,18,20,22,24],extens:[9,29],extract:[26,29],extrem:[22,29],f1:[6,21,25],f5hmz4:20,f:[5,6,20,21,24,29],fabrigar:29,facet:18,facil:22,factor:22,faculti:29,fail:[22,29],falciparum:29,fale:29,fals:[5,20,24],falsearrai:20,falsexarrai:20,famili:29,fanello:29,fanni:29,fanzana:29,far:[22,29],farafenni:29,faranah:29,farm:29,farmland:29,faso:[2,7,9,12,15,16,20,21],faster:[5,20,24],fastq:6,father:29,fatti:20,feasibl:22,feb:[24,25],februari:29,fed:29,feel:[5,20],fell:22,femal:[5,20,22,29],fenitrothion:29,few:[6,21,25,29],fewer:22,field:[5,17,25,26,29],file:[6,21,22,25],fill_valu:24,filter_pass:[5,20,24],find:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,21,24,26,29,30],fine:29,finnerti:29,first:[0,1,5,6,13,20,21,22,24,25,29],fish:29,fit:[5,20,22],five:[22,29],fix:[28,29],flag:[1,2,3,5,6],flat:29,float320:20,float32:[5,20,24],float32dask:[5,20,24],flood:29,floor:29,florenc:29,flow:[5,14,20,29],focu:[1,2,3,8,9,10,11,12,13,14,15,16,17],focus:[18,22],fofana:29,fold:22,folder:[6,21,25],follow:[5,6,7,10,11,20,21,22,24,25,26,29,30],fondazion:29,fontain:9,fontenil:29,fontenillei:[15,16],food:29,forest:29,form:[1,2,3,8,9,10,11,12,13,14,15,16,17,20,29],format:29,fort:[0,29],forum:25,fots:29,fouet:29,found:[0,1,2,3,5,8,9,10,11,12,13,14,15,16,17,20,21,24,29,30],four:[2,15,22,29],fourth:29,fr:[7,20,21,29],fraction:22,fragment:[22,29],franc:29,francisco:29,franck:29,frank:29,franklin:29,freder:29,free:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,24,26,30],freeli:30,frequenc:[20,22,29],from:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,26,28,29,30],frq_bf:20,ftp:[6,21],full:[1,22],funestu:[1,2,3,4,5,6,14,29],funestusxarrai:5,further:[5,6,20,21,22,24,29],furvela:29,futur:[1,2,3,5,22,30],g3:29,g:[5,6,7,20,21,22,24,29],ga:[0,1,5,6,7,16,17,20,21,29],gaardian:[1,10,12,15],gabakoro:29,gabon:[0,1,7,15,16,17],gabu:29,gado:29,gamb_colu:[20,21,22],gamb_colu_arab:[5,20,21,22],gambcolu:21,gambia:[1,2,3,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,23,28],gamez:29,gap:14,gatk:22,gaussian:22,gaussianhmm:22,gb:[6,20,21,24],gbadolit:29,gbullung:[5,6],gc:[5,6,20,21,22,24,25,26,30],gcloud:30,gcx1:[7,9,13,17,20],gcx2:[7,13,17,20],gcx3:[7,20],gcx4:[15,16],gel:[26,29],gender:[5,6,20,21,24],gene:[5,14,17,20,22,29],gene_cnv:20,gene_cnv_frequ:20,gene_contig:20,gene_descript:20,gene_end:20,gene_id:20,gene_nam:20,gene_start:20,gene_strand:20,gene_window:20,gener:[1,2,3,5,6,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,29],genet:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,22,24,25,26,29],genom:[5,6,18,20,21,28,29,30],genome_sequ:24,genotyp:[22,29],genotypedaskarrai:[5,20,24],gentil:29,gentra:29,geoff:29,geograph:29,georg:29,get:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,27,30],gh01:[5,6],gh02:[5,6],gh03:[5,6],gh04:[5,6],gh05:[5,6],gh06:6,gh07:6,gh08:6,gh09:6,gh:[0,1,5,6,7,10,11,12,15,20,21,29],ghana:[0,1,5,6,7,10,11,12,15],ghtm:29,gib:5,gilbert:29,gilli:29,github:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26],give:[5,6,20,21,24,25],given:[5,6,7,20,21,22,24,25,29],glacial:29,global:[0,29],globe:30,glucos:29,gm:[7,13,17,20,21,22,29],gmail:[29,30],gn:[7,9,20,21,29],godefroi:29,godfrai:29,goff:29,gome:29,googl:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26],googleapi:[21,25],gov:29,govend:29,gowelo:29,gp:26,gprmac2:20,gq:[6,7,20,21,22,29],gr:29,gradient:29,gradual:29,grant:[29,30],graph:5,grassland:29,grau:29,gravid:29,greater:[5,20,22],greenhous:29,ground:29,group:[22,29],groupbi:[5,20],grove:29,grow:29,gs:[5,6,20,21,25],gste3:22,gstu4:22,gsutil:[6,21,25,30],gt:[5,20,24],gt_cohort:[5,20,24],gtd:24,guel:29,gui:29,guid:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,21,22,25,26],guillaum:29,guindo:29,guinea:[7,9,15,17,22],gupanarigu:[5,6],gw:[7,20,21,29],gz:[6,21,25],gzip:21,h:29,ha:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,28],had:22,half:[22,29],hamdalai:29,hamlet:29,han:29,hand:22,handl:[22,29],haplotyp:[1,2,3,8,9,10,11,12,13,14,15,16,17,28],haplotypedaskarrai:[5,20],hard:[5,6],harold:29,harvard:22,hatch:29,have:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,28,29],hdl:29,hdy:29,head:[5,6,20,21,25],health:[1,2,3,8,9,10,11,12,13,14,15,16,17,29,30],held:22,help:[1,2,3,7,8,9,10,11,12,13,14,15,16,17,30],henc:21,henk:29,henri:29,here:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,24,25,30],hereaft:22,hered:29,het:22,heterogen:[13,29],heterozyg:22,heterozygos:21,heterozygot:22,hi_:21,hidden:22,hierarchi:[6,21],high:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,26,29],higher:30,highest:[22,29],highland:29,highli:22,higien:29,hilari:29,hill:29,hinxton:29,hiseq:22,hmmlearn:22,hof:29,hold:[6,21],home:[6,21,25],hope:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26],hopefulli:[0,7],hour:29,hous:29,how:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,24,25,26],howel:29,howev:30,ht:[5,20],ht_cohort:[5,20],http:[5,6,21,25,26,29,30],hugh:29,human:[17,29],humid:29,hundr:[5,20],hung:29,hunt:29,hut:29,hutchinson:29,hyacinth:29,hybrid:29,hyg:29,hygien:29,hyperendem:29,hyperparamet:22,i:[5,20,22,24,29,30],ibrahima:29,icer:8,icon:[5,20,24],id:[5,20,25],ident:29,identif:29,identifi:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,29],ig:29,igor:29,ihmt:29,ilboudo:29,illo:29,illumina:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26],illustr:[5,20,24],immedi:29,immo:29,immunolog:29,imp:29,impact:[1,14,22],imperi:29,implement:22,implic:[1,13,14,17],improv:29,inc:29,incipi:29,includ:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,28,29,30],inclus:22,incorrect:28,increas:[20,22,29,30],increment:22,indel:22,indelrealign:22,independ:[7,22,29],index:[5,6,20,21,24,25],indic:[5,20,22,24,29],individu:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29],indoor:29,infect:[1,11,29],infecti:29,infer:[5,6,20,21],infett:29,inform:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,30],informat:22,inhabit:29,inhamban:29,inher:29,inherit:[5,20,22],inhibitor:20,initi:[22,29],inocul:29,insect:29,insectari:29,insecticid:[1,2,3,8,9,10,11,12,13,14,15,16,17,20,21,29],insecticida:29,insert:22,insid:[0,29],inspect:[6,21,22,25],instal:[0,5,20,24,30],instanti:5,instar:29,institut:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,21,22,25,26,29],instituto:29,int16:[5,20,24],int16dask:[5,20,24],int32:[5,20,24],int32dask:[5,20,24],int6423:20,int643426:20,int649985:20,int64:[5,20],int82:20,int8:[5,20,24],int8dask:[5,20,24],integ:[5,20,24],integr:[29,30],intend:[6,21,25],intens:29,interact:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,24,26],interest:[5,6,20,21,22,24],intermedi:[20,21,22,29],intermediate_arabiensis_gambia:20,intermediate_gambiae_coluzzii:20,intern:[8,29],interpret:[18,20],intersect:22,interspers:29,interv:22,intervent:[1,14,29],introduc:29,introduct:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,20,21,26],introgress:[9,22,29],invari:24,invers:[22,29],investig:[1,13,14,22],invitrogen:29,involv:[5,7,20,22,29],iowa:5,iran:29,ird:29,irrig:29,irss:29,is_segreg:[5,20,24],isel:[5,20],island:17,isol:29,issu:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,20,21,26,30],issue33725:6,istituto:29,itali:29,italia:29,iter:22,its:[22,29],ivoir:[7,10,14],j:29,jaenson:29,jaim:29,jame:29,jan:[24,25],janet:29,januari:29,jarjav:29,jawara:29,jean:29,jenkin:29,jinja:29,joachim:29,joao:20,johannesburg:29,john:29,johnson:29,jointli:18,jone:29,jorg:29,joseph:29,journal:[1,2,3,8,9,10,11,12,13,14,15,16,17,29],jovin:29,jpinto:29,jubil:29,jul:[24,25],juli:29,julia:29,juliana:29,jun:22,june:[9,29],junqueira:29,just:[6,7,21],k2:29,k4:29,k6:29,k:[20,24,29],kaaya:29,kababoug:29,kabagh:29,kabr:29,kabula:[15,29],kajo:[1,16],kalataba:29,kamali:29,kamau:17,kamdem:29,kamija:29,kampala:29,kamya:29,kanungu:29,kardo:29,karyotyp:29,kassena:[1,11,15],kavish:29,kayondo:[1,16],kazemb:29,kb663610:24,kb663611:24,kb663622:24,kb663633:24,kb663644:24,kb663655:24,kb663666:24,kb663677:24,kb663688:24,kb663699:24,kb663710:24,kb663721:24,kb663722:24,kb663733:24,kb663744:24,kb663755:24,kb663766:24,kb663777:24,kb663788:24,kb663799:24,kb663810:24,kb663821:24,kb663832:24,kb663833:24,kb663844:24,kb663855:24,kb663866:24,kb663877:24,kb663888:24,kb663899:24,kb663910:24,kb663921:24,kb663932:24,kb663943:24,kb663955:24,kb664054:24,kb664165:24,kb664255:24,kb664266:24,kb664277:24,kb:[20,21,24],kdr:29,ke:[0,1,5,6,7,17,20,21,29],keep:0,kei:29,keita:29,keith:29,kela:29,kemri:29,kenji:29,kenneth:29,kenya:[0,1,7,9,11,17,22],kenyan:29,keppel:29,kept:29,kern:29,kernel:5,kerr:29,kevin:29,kh:25,kiaxi:29,kib:[5,6],kidima:29,kientega:16,kigozi:29,kihihi:29,kilama:29,kilamba:29,kilifi:29,kilimanjaro:29,kima:16,kimberli:29,kingdom:29,kinyoki:29,kisinza:29,kissidoug:29,kisumu:29,kit:29,kitau:29,kleang:[24,25,26],kleinschmidt:29,km:29,knockdown:29,know:[0,5,6,20,21,24,25],known:[0,7,20,22,29],koekemo:[0,5,6],koffi:14,koforidua:29,komaswa:29,kombila:29,konat:29,kone:29,koraboh:29,kou:29,koudou:29,koulikoro:29,koundara:29,kovana:29,kuklinski:29,kuma:29,kumbungu:5,kunda:29,kv:24,kwang:29,kwiatkowski:29,kyann:29,l3:29,l995f:29,l:[13,29],la:29,lab:[7,20,29],label:[20,22,28,29],laboratoir:29,laboratori:[26,29],lagdo:29,lai:29,laid:29,lake:29,lama:9,lambda:29,land:29,landscap:29,lane:22,larg:[6,21,25,29,30],larger:22,largest:24,larva:29,larval:29,lassana:29,late:[24,25],later:29,latitud:[5,6,20,21,24,25,26],lauderdal:0,launch:[5,20,24],laurent:[24,25,26],lavoi:29,lawniczak:[0,1,11],lawrenc:29,layer:5,le:29,lead:22,leaf:22,learn:22,least:22,leav:22,led:[0,26],leffler:22,leg:29,legoff:29,lehmann:[8,10],leibala:29,len:[5,20,24],length:[21,24,29],less:[5,20,22,29],let:[5,20,24],letter:[5,7,20],level:29,libitum:29,librari:22,librevil:29,life:29,light:29,like:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29],likelihood:22,limit:[5,20,22,29],lindsai:29,line:[6,21,25,30],link:[6,21,25],linux:[6,21,25],lisboa:29,lisbon:29,list:[0,1,2,3,6,7,9,10,11,12,13,14,15,16,17,21,29],literatur:[1,2,9,15,16,17],live:29,liverpool:[22,29],lizett:5,ljmu:29,ll:[5,20,24],llin:[14,16],llineup:[14,16],lo_:21,load:[5,20,24],lobo:29,loc:[5,20],loc_cohort:24,loc_cohort_sampl:[5,20],loc_funestu:5,loc_gambia:20,loc_pass:[5,20,24],loc_seg:[5,20],local:[5,6,20,21,22,24,25,26,29],locat:[0,5,6,7,20,21,22,24,25,26,29,30],loci:[20,21,29],locu:29,log:30,login:30,logist:22,london:29,longipalpi:1,longitud:[5,6,20,21,24,25,26],longitudin:26,look:18,lookseq:29,loua:29,loughlin:29,love:[5,6,20,21,24,25],low:[5,6,20,21,22,24,29],lower:[22,29],loyc:29,lshtm:29,lstm:[8,20],lstmed:29,lt:[5,20,24],lua001:20,lua002:20,lua004:20,lua006:20,lua007:20,lua047:20,lua049:20,lua051:20,lua061:20,lua078:20,lua:20,lua_colu_2009:20,lua_colu_2009_04:20,lua_luanda_colu_2009:20,lua_luanda_colu_2009_04:20,luanda:[20,29],luc:29,luca:[22,29],lund:29,lutt:29,lydi:29,lynd:29,m:[6,20,21,29],mabogini:29,mac:29,macenta:29,machin:[22,30],maco:6,madagascar:[17,29],made:[1,2,3,8,9,10,11,12,13,14,15,16,17,20,21,22,29],madina:29,magesa:29,mai:[0,5,6,7,20,21,22,24,25,29,30],maiga:29,mailto:30,main:29,mainland:29,mainli:29,maintain:29,mair:29,majet:29,majidah:29,major:[0,1,11,14,15,17,22,26,29],make:[0,5,20,22,24],makumira:29,malaria:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,18,26,29,30],malariagen:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,26,30],malariagen_data:[0,4,5,19,20,23,24,28],malatti:29,malawi:[0,1,7],male:[5,20,22,29],mali:[1,7,8,9,10,12,17],malian:[8,10],malima:29,mamad:29,manag:29,mancini:29,manda:29,mango:29,mani:[0,5,24],manifest:[5,6,20,21],mansk:29,manual:[22,29],manufactur:22,map:[0,7,21,22,25,29],mara:0,maranda:29,marc:29,march:29,marcia:29,marco:29,mari:29,maria:29,mark:[6,21,25,29],marker:21,markov:22,marsh:29,martin:[20,29],maryam:29,maryland:29,maryvonn:29,mask:[5,20,24],massiv:29,master:29,masu:29,match:[5,20,24],mater:29,materi:18,mathanga:29,mathurin:29,matia:29,matiya:29,matowo:29,maureen:29,mawejj:29,max_af:20,max_allel:[5,20,24],maximum:22,maxwel:29,mayo:29,mayott:7,mb:[20,21,24],mbogo:29,mbp:[6,21],mburu:29,mccann:29,md:[6,29],mead:29,meal:29,mean:[5,6,20,21,22,29],meant:22,med:29,median:[22,29],medic:29,medicin:[22,29],medicina:29,mehaffei:29,meillon:29,mela:[9,15,17,29],melissa:29,member:[7,22,29],memori:[5,20,24],mendelian:[22,29],mendez:29,menu:30,merg:[6,21,22],merged_vari:[6,21],meru:[9,17,29],mesa:29,mesamalaria:29,meso:29,meta:[5,6,20,21,24,25],metadata:[7,22,26],method:[5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,26,27,29,30],methyl:29,metric:22,mg:21,mib:5,michael:29,michel:29,micro:29,microb:29,microbiolog:29,microsatellit:29,microscop:29,midega:29,might:[6,21],migrat:[8,10],mile:[22,29],million:[5,20],milwauke:29,min:[6,21],miniatur:29,minim:22,minimis:30,minimu:[25,26,28],minimum:22,minimus1:24,minja:29,minneapoli:29,minut:[5,20],miss:[5,20,22,24],mit:22,mivegec:29,mix:29,mkdir:[6,21,25],ml:[7,8,10,20,21,26,29],mmp:29,mn:29,modal:[20,22],modar:29,mode:22,model:[5,6],modif:22,modifi:29,mok:[24,26],mol:29,molbev:29,molecular:29,monicah:29,monitor:[0,15,29,30],monomtenga:29,month:[5,6,20,21,24,25,29],montpelli:29,moor:29,mopti:29,more:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,26,29,30],moriboboug:29,morn:29,morpholog:29,mortal:29,mose:29,mosha:29,moshi:29,mosquito:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29,30],most:[20,21,22,29,30],mother:29,motinho:5,mount:29,mourou:29,moussa:29,mouth:29,mozambican:29,mozambiqu:[0,1,5,7],mozf_1314:5,mozf_1315:5,mozf_1317:5,mozf_1319:5,mozf_1323:5,mq:[6,21,22],mra:29,mrcg:29,mrtc:29,msangi:29,msx087:29,mtsanga:29,much:29,muheza:29,muleba:[1,14,29],multi:[0,1,5,6,9,12,13,15,16,17,20,21,24,25,29],multiallel:22,multipl:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,21,26,29],multiplex:22,multipli:22,multiprocess:6,multithread:6,munhenga:[14,17],municip:29,musa:29,muscarin:20,museum:29,muskavitch:29,must:20,mutat:[22,29],mve:29,mw:[1,7,20,21,29],mwangangi:29,mwesigwa:29,mweya:29,mybind:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20],myriad:29,mz:[0,5,6,7,20,21,29],mzilahowa:29,n:[5,6,20,21,22,24,25,29],n_pass:24,n_pass_seg:[5,20,24],n_site:24,na:29,nacion:29,nagongera:29,nakasero:29,name:[6,20],nan:[20,24],nanarrai:20,nankana:[1,11,15],nat:29,natacha:29,nation:[26,29],natur:[0,7,22,29],nbesansk:29,nbsp:[24,26],ncbi:29,ncomms1672:29,nd:29,ndarrai:[5,20,24],neafsei:[22,29],nearbi:29,nearest:22,nebul:22,necessarili:[5,20],need:[1,2,3,5,6,20,21,24,30],neg:22,neighbourhood:29,neil:29,nelson:29,net:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,29,30],netherland:29,network:[5,6,13,15,27,30],nextec:26,ng:[1,16,22],ngayo:29,ngwa:17,niaid:[8,26],niang:9,niar:29,nich:29,nicola:29,niel:9,nigeria:[0,1,16,17],night:29,nih:[8,26,29],nimr:29,niono:29,njabakunda:29,njau:29,nkolondom:29,nlm:29,no_cov:21,node:[5,20,22,24],nohal:29,nomenclatur:29,non:[5,6,20,21,22],none:[5,22],nonmajor:[6,21],noor:29,nora:29,norm:[1,2,3,8,9,10,11,12,13,14,15,16,17,22],normal:[5,20],normalis:22,north:29,northeast:29,northern:5,note:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,30],notebook:[5,6,20,21,24,25],notr:29,noufou:29,nov:[24,25],nova:29,novel:29,novemb:[8,10,11,12,13,14,15,16,29],novo:22,now:[5,20,24],np:[5,20,24],np_fune_2017:5,np_fune_2017_07:5,np_fune_2017_08:5,np_fune_2017_q3:5,np_kumbungu_fune_2017:5,np_kumbungu_fune_2017_07:5,np_kumbungu_fune_2017_08:5,np_kumbungu_fune_2017_q3:5,np_tolon_fune_2017:5,np_tolon_fune_2017_07:5,np_tolon_fune_2017_08:5,np_tolon_fune_2017_q3:5,nuclear:22,nucleotid:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29],number:[0,1,7,8,9,10,11,12,13,14,15,16,17,24,26,28,29],numer:29,numpi:[5,20,24],nwakanma:29,nyado:29,nyangweso:29,nzerekor:29,nzovu:29,o:[6,20,29],object:[0,5,6,7,20,21,22,24,25],objectdask:[5,20],objectnan:20,observ:[5,6,20,21,22,24],observatori:[0,5,6],obtain:[5,6,20,21,22,29,30],occur:[22,29],occurr:29,oceac:29,ochieng:29,ochomo:[0,5,6],octob:29,offspr:29,often:29,oh:29,oil:29,ok:21,okedi:29,okello:29,okfr:1,okumu:[0,1,2,3,5,6],okyereko:29,olotu:29,oloughlin:[1,12,29],omitola:[1,16],omol:[1,16],onc:22,one:[1,2,5,6,8,9,16,20,21,22,24,26,27,29],ones:[5,6],ongo:[1,2,3,8,9,10,11,12,13,14,15,16,17],onli:[0,5,6,7,20,21,22,24,29,30],onto:22,open:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26,29],openli:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26],oper:[5,6,20,21,22,24],operation:18,opondo:[13,29],optic:29,optimis:[22,30],option:[6,21],order:[5,20,28],org:[6,26,29],organis:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,29,30],organophosph:29,origin:[1,2,3,8,9,10,11,12,13,14,15,16,17,22,29],original_sample_id:[24,25],os:29,other:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29,30],otherwis:[1,2,3,8,9,10,11,12,13,14,15,16,17,22,29],ouagadoug:29,ouassorola:29,oulena:29,oumou:29,our:[1,2,3,5,6,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,30],out:[0,5,7,20,22,24,26,29],outbreak:[1,2,3,8,9,10,11,12,13,14,15,16,17],outdoor:29,output:[5,6,20,21,22],outsid:[0,22,29,30],ovari:29,over:[0,5,6,20,21,22,24,26,29],overgaard:29,overlap:[5,6,20,21,22],overnight:29,overview:[0,7],ow:29,own:[0,6,7,21,29],ox1:29,ox:29,oxford:29,oxfordmartin:29,p450:29,p:[5,20,24,29],p_fune_2015:5,p_fune_2015_08:5,p_fune_2015_q3:5,p_palma_fune_2015:5,p_palma_fune_2015_08:5,p_palma_fune_2015_q3:5,paaijman:[0,5,6],packag:[4,5,19,20,23,24,28],page:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,26,27,29],pain:29,pair:[5,20,22,29],pairwis:22,pala:[21,29],palm:29,palma:5,paludism:29,pamca:[1,2,13,14,15,17,18],pamgen:[9,13,15,17],pan:[13,15],panda:[5,20,24],panel:[5,20,22],paper:[0,26,29],paracentr:[22,29],parallel_process_count:6,paramet:[5,20,22],parasit:[1,11,15,17,29],parasitolog:[26,29],parassitologia:29,parensi:1,parent:[5,20,22,29],pari:29,park:29,parsimoni:29,part:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,21,26,29],parti:30,particular:[5,6,20,21,22,24,25,29],particularli:22,partit:29,partner_sample_id:[5,6,20,21,24,25],pascal:29,pasqual:29,pass:[5,20,21,22],pasteur:29,patch:28,path:[6,21,25],pathogen:[1,2,3,8,9,10,11,12,13,14,15,16,17],patric:29,patricia:29,patrick:29,pattern:22,patton:29,paul:29,pc1:22,pc2:22,pca_cohort:[24,25],pcr:29,peak:29,pedigre:22,peopl:29,per:[6,21,22],per_sampl:[6,21],percentag:22,percentil:22,perenni:29,perform:[5,18,20,21,22,24,29,30],peri:29,perman:29,permethrin:29,permiss:[1,2,3,8,9,10,11,12,13,14,15,16,17,30],permit:[0,1,2,3,8,9,10,11,12,13,14,15,16,17],peter:29,petrarca:29,pgen:29,phase:[1,5,6,20,21,27,29],phenol:29,phenoloxidas:20,phenotyp:13,philbert:29,philip:29,philippa:29,phiri:29,phylogenom:9,physic:[5,20,24],pie:29,pimperena:29,pinto:[20,29],pip:[0,5,20,24],pipelin:[6,21,22],pipini:29,pirimipho:29,pivot_t:24,place:[5,6,20,21,24,25,29],plan:[0,30],plantat:29,plasmodium:[0,1,16,17,29],plastic:29,plate:[26,29],platform:22,plausibl:22,pleas:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,30],plo:29,ploidi:[5,20,24],plot:[18,29],pmc2988034:29,pmc3543752:29,pmc3606099:29,pmc4124135:29,pmc:29,po:[5,20,24,29],point:22,polici:30,pollut:29,polymeras:29,polymorph:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29],polyten:29,pombi:29,pool:29,popul:[1,2,5,11,14,15,17,20,24,25,29],portug:29,posit:[5,6,20,21,22],possibl:[5,20,22,24,29],potenti:[22,29],poupardin:29,pour:29,power:[5,20],pradin:29,praso:29,pre:[1,2,3,5],preah:[24,25,26],precis:[7,22],predict:22,predomin:29,prefix:[6,21,25],preliminari:[21,29],prepar:[1,2,3,8,9,10,11,12,13,14,15,16,17,22,29],presenc:[0,1,5,16,17,20,22,29],present:[0,21,22,25,29],preserv:29,presum:22,previou:[22,29],previous:[22,29],primari:[1,2,3,8,9,10,11,12,13,14,15,16,17,29],primer:29,princip:[17,22],principl:0,print:[5,20,24],prior:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,29,30],probabl:[6,21,22],probe:29,problem:6,problemat:29,proceed:29,process:[22,29],produc:[5,6,22,29],product:22,progeni:[22,29],programa:29,programm:[1,2,13,14,15,17,29],progress:[5,20,24],progressbar:[5,20,24],project:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,27,29],prone:29,proport:[22,29],prot:20,protein:20,protocol:[22,29],protopopoff:29,provid:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,27,28,29,30],provinc:[26,29],provis:30,proxim:[5,6,20,21,29],pt:29,pubblica:29,publicli:[1,2,3,5,6,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25],publish:[0,29],pubm:29,puddl:29,pupa:29,pure:29,puregen:29,purpos:[7,26,30],pursat:26,put:[20,22],pv:[6,21,24,25],py:[20,24],pypi:24,pyrethroid:29,pyrethrum:29,pysam:22,python:[4,5,6,19,20,23,24,28],q10:21,q30:21,q7pkf8:20,q:[0,5,20,24,29],q_mean:21,q_std:21,qiagen:29,quadriallel:24,quadriannulatu:[9,17],qualiti:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,26],quarterli:26,queri:[5,20,24],question:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,20,26,30],r:[6,21,25,29],radiat:29,rain:29,raini:29,rais:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26,29],ramphul:29,ran:[21,25],random:22,randomis:29,randomli:[22,29],rang:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,26,29],ranson:29,rapid:[1,2,3,8,9,10,11,12,13,14,15,16,17],rare:22,rasman:29,rasmussen:29,ratanakiri:26,rate:[22,29],rather:[1,2,3,8,9,10,11,12,13,14,15,16,17,22],ratio:22,rational:[1,2,3,8,9,10,11,12,13,14,15,16,17],raw:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,26],raymond:29,rdna:29,re:29,reach:[29,30],reaction:29,read:[5,6,24,28,29],readi:[21,25,27],readm:6,realign:22,realignertargetcr:22,rear:29,reason:30,rebuild:9,receiv:22,recent:[5,20,29],receptor:20,recherch:29,recogn:29,recomput:22,record:[20,22,29],reddi:29,reduc:29,refer:[5,20,22],reflect:29,reg:20,regard:[5,6,20,21,22,24],regardless:[6,21],regier:29,reginald:29,region:[5,6,7,20,21,22,24,25,29,30],regna:29,reidenbach:29,rel:[21,22,29],relat:6,related:22,releas:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,25,26,29,30],relev:18,reliabl:[5,6,20,21,22,24,29],remain:[1,2,3,5,8,9,10,11,12,13,14,15,16,17,20,22,30],rememb:7,remov:[6,21,22,25,29],rep:29,replac:22,repo:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26],report:[18,21,22,29],repositori:[1,2,3,8,9,10,11,12,13,14,15,16,17,22],repres:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,22,24,29],republ:[0,1,7,13],request:21,requir:[5,6,20,21,22,24,25,29,30],rerun:28,research:[0,7,8,26,29],reset_index:[5,20],residu:29,resist:[1,2,3,8,9,10,11,12,13,14,15,16,17,20,21,29],resolv:[5,20,21,22],resourc:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,26,27,28,30],respond:[1,2,3,8,9,10,11,12,13,14,15,16,17],respons:21,rest:29,restart:5,restrict:29,result:[5,6,18,20,22,26,29],retain:22,retriev:29,reveal:[9,26,29],review:29,rflp:29,ribosom:29,ric:29,rice:29,richard:29,ridl:29,riehl:29,rippon:29,risk:29,ritha:29,river:29,riversid:29,rk1:24,rk2:24,rn:[6,21],rna:29,rnalat:29,road:29,roadsid:29,robert:29,rodolph:29,rodrigu:29,roelant:29,rohatgi:29,roma:29,romain:29,rome:29,root:[6,21,22],rosario:29,row:[5,6,20,21,24,25],rowland:29,rsync:[6,21,25],rua:29,run:[6,21,22,24,25,29,30],runtim:30,rural:29,russia:29,ruth:29,s12879:29,s12936:29,s1:[5,20,24],s1dask:[5,20,24],s24:24,s24dask:24,s3:[6,21,25],s:[0,1,2,3,5,8,9,10,11,12,13,14,15,16,17,20,21,22,24,26,29],sabatini:29,sacriba:29,safim:29,sagnon:29,sahara:29,sahel:[8,10],salaam:29,sama:29,samantha:29,samba:29,same:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,22,24,29],sampl:28,sample_count:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21],sample_coverage_vari:[5,20],sample_id:[5,6,20,21,24,25],sample_is_high_vari:[5,20],sample_metadata:[5,20,24],sample_queri:20,sample_set:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21],samples_phas:[5,20],samson:29,samuel:[5,6,29],san:[24,26,29],sanger:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,21,22,25,26,29],sanger_sample_id:[24,25],sanita:29,sankar:29,santolamazza:29,sao:17,sapienza:29,sarah:29,sare:29,savanna:29,savannah:29,save:21,saya:[24,26],sc_20220908:[5,6],scale:29,scan:[5,20],scatter:29,school:[22,29],sci:29,scienc:[29,30],scientif:18,scientifiqu:29,scikit:[5,20,22,24],score:29,scott:29,screen:[0,1,16,17,29],sea:29,search:21,season:[1,14,24,25,29],second:[5,6,20,22,24,29],section:[20,21],see:[5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,24,25,26,28,29,30],segreg:[5,20,22],sekou:29,select:[5,17,20,21,22,24,29,30],semi:29,seneg:9,seni:29,sent:21,separ:[0,5,6,20,21,22,26,29],septemb:29,seq:24,sequenc:[5,6,20,24,27,29],servic:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,26,30],set:[22,24],set_capt:24,set_index:[5,20],seven:29,sever:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,21],sex_cal:[5,6,20,21],shandala:29,shape:[5,20,24],shapeit4:22,sharakhov:29,sharakhova:29,share:[1,2,3,8,9,10,11,12,13,14,15,16,17,22],sharp:29,sheet:29,shelter:29,shik:29,should:22,show:25,shown:[5,20,24,29],shrubland:29,side:29,sidi:29,signal:[5,20],signific:22,significantli:29,silenc:[5,20],silica:[26,29],silwood:29,simard:29,similar:22,simon:29,simpl:[24,29],simpli:20,simultan:29,sinc:29,sindato:29,sinex:29,singl:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29],singleton:22,site:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,25,26,29],site_filt:[5,6,21],site_filters_analysi:5,site_mask:24,six:[22,29],size:[5,20,22],sj:29,skew:22,skip:30,sl5:29,slice:[5,20,24],slightli:22,slope:29,slotman:29,small:[1,2,22,24,29],smith:29,sn:9,snounou:29,snow:29,snp:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26,28],snp_call:[5,20,24],snp_genotyp:[6,21],snp_genotypes_vcf:[6,21,25],snp_haplotyp:[6,21],so:[5,6,20,21,22,24,30],soc:29,softwar:[5,20],sogolomboug:29,solut:29,solv:29,some:[0,5,6,7,20,21,22,24],soon:30,sort:29,sourc:[20,22,29],souroukoudinga:29,sousa:29,south:[1,9,14,17,29],southeast:26,southern:29,sow:29,space:[21,22],spatiotempor:0,speci:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,24,26,29],special:[20,29],speciat:29,species_aim:21,species_calls_aim_20220528:21,species_gambcolu_arabiensi:21,species_gambiae_coluzzii:21,specif:[0,5,6,7,20,21,22],specifi:0,specimen:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,22,24,25,26,29],split_large_chunk:[5,20,24],sporozoit:29,sprai:29,spread:[1,13,22,29],squar:22,srep46451:29,ss:29,st:[24,25,26],staedk:29,staff:22,stalker:29,stand:[5,20],standard:[29,30],start:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,26,27],state:[1,2,3,5,6,8,9,10,11,12,13,14,15,16,17,20,21,24,25,29],station:29,statist:[5,6,18],statu:[22,29],steen:29,step:[6,22],stephan:29,stephani:29,stephen:29,steve:29,steven:29,still:6,stlaurent:25,stochast:22,storag:[5,6,20,21,24,25,26,30],store:[5,6,20,21,24,25,26,29,30],strategi:[1,2,3,8,9,10,11,12,13,14,15,16,17,29],street:29,strengthen:14,string:[5,20],strongli:29,structur:[0,6,14,17,21,24,25,29],studi:[5,6,20,21,24,27],study_id:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17],study_url:[5,6],style:24,subcounti:29,subdivid:21,subgroup:29,subject:[0,5,7,20,22,29,30],submit:[0,22,30],subsampled_cohort:[24,25],subsect:[6,21,22],subsequ:29,subset:[6,21,22,24],substanti:[21,30],suburb:29,suburban:29,success:22,successfulli:22,sudan:29,sudanian:29,suffici:[6,21],suffix:7,sugar:29,suggest:29,suiss:29,suitabl:[20,21,22,24],sum:24,summari:[5,6,20,24],summaris:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,20],suna:29,sunset:29,supplement:29,support:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,22,30],sur:29,surround:29,survei:29,surveil:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,26,30],suscept:29,suspend:30,swampland:29,swarm:29,sy:29,sympatri:29,synchron:[6,21],system:[6,21,25,29],systemat:29,t:[5,6,20,21,22,24,29],tab:[6,21],tabix:[6,21],tabl:18,tag:22,takan:29,take:[5,6,20,21,22],taken:29,takken:29,takoradi:29,talisuna:29,tankonjala:29,tankular:29,tanzania:[0,1,2,3,7,9,15,17,22],tanzanian:29,tarbiat:29,target:[1,12,22,29],targetmalaria:29,tarim:29,task:[20,24],taxa:29,taxon:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20],tb:20,tbi:[6,21],td:24,team:22,tech:29,technician:29,technolog:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26],tehran:29,templat:29,temporari:29,temporarili:30,tennessen:16,terlouw:29,term:[5,20],termin:[6,21,22,25],terra:[22,30],test:29,tetramin:29,text:[6,21],tg:10,than:[1,2,3,5,8,9,10,11,12,13,14,15,16,17,20,22,29],thank:[22,29],thei:[0,6,21,29,30],them:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17],themba:29,themselv:5,therefor:[24,29],thes:[6,21],thesi:29,thi:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,27,29,30],thicket:29,thierri:29,third:[5,7,20,24,29,30],thmar:[24,26],thoma:29,those:22,threat:[1,2,3,8,9,10,11,12,13,14,15,16,17],three:[5,6,7,20,21,24,26,29],threshold:22,thrive:29,through:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26,29],throughout:[5,6,20,21,22,24,25,29],thu:[5,20,22],thymin:[5,20],tiassal:29,tibati:29,tienegueboug:29,time:[0,5,6,20,21,24,25],times2784:20,times36:5,times656:5,times82:20,tissu:29,tjmidega:29,to_haplotyp:[5,20],togeth:[20,21,22],togo:10,tolon:5,toma:29,tome:17,tomsk:29,took:[22,29],tool:[6,21,25],top:[5,20,22,24],topographi:29,tororo:29,torr:29,total:[7,22,24],touch:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25],toumani:29,tour:29,town:29,townson:29,track:29,trai:29,train:[18,22,29],tran:29,transect:29,transfer:[5,20,24,30],transit:[22,29],transmiss:29,transmit:29,transport:29,traor:29,trap:29,tree:[5,6,22,29],trembl:20,trial:[17,29],triallel:24,trim:[6,21],troco:29,trop:29,tropic:[22,29],trstmh:29,truli:22,trust:29,tsv:[6,21],tube:[26,29],tumaini:29,tungu:29,turn:29,twenti:29,twice:22,twifo:29,two:[5,6,7,17,20,22,26,29],type:[1,2,3,5,6,8,9,10,11,12,13,14,15,16,17,20,21,24,29],tz:[0,1,2,3,5,6,7,15,20,21,29],u24:20,u24dask:20,u36:5,u36dask:5,ug:[1,7,11,14,16,20,21,29],uganda:[0,1,7,11,14,16,17],uint8:[5,20,24],uint8dask:[5,20,24],uk:[0,6,8,21,25,29],umberto:29,umr:29,unassign:[7,8,9,10,11,12,13,14,15,16,17],unbalanc:22,uncertain:22,under:[5,22,29],understand:[0,13],undertaken:[22,29],unexpect:30,unifiedgenotyp:22,union:17,uniprotkb:20,uniqu:[20,22,24],uniroma1:29,unit:[5,6,20,21,24,25,29],univ:29,univers:29,universidad:29,unl:29,unless:[1,2,3,8,9,10,11,12,13,14,15,16,17,29],unreli:22,unstabl:29,until:29,unusu:29,up:[5,6,20,21,22,24],updat:5,upgrad:30,upland:29,upload:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17],upon:[0,29],urban:29,url:[5,6,20,21,25,29],urvashi:29,us:[6,18,21,24,25,28,29],usa:[8,26,29],user:[6,30],usual:[21,22,29],v1:[6,25],v3:21,v:[22,29],vaccin:29,valencia:29,valid:22,valu:[5,20,22,24,25,29],valuabl:[0,7,26],vamsi:29,van:29,vaneedeni:1,vari:29,variabl:[5,20,24],varianc:[5,6,20,21,22],variant:[5,6,20,21,24,27,28],variant_allel:[5,20,24],variant_ciend:[5,20],variant_cipo:[5,20],variant_contig:[5,20,24],variant_end:[5,20],variant_endbreakpointmethod:20,variant_filter_pass:[5,20,24],variant_filter_pass_:[5,20],variant_filter_pass_arab:20,variant_filter_pass_funestu:5,variant_filter_pass_gamb_colu:20,variant_filter_pass_gamb_colu_arab:20,variant_id:[5,20],variant_posit:[5,20,24],variant_region:20,variant_startbreakpointmethod:20,variat:[7,22,29],variou:[5,20,24],vast:22,vb:20,vbs09378:[24,25],vbs09382:[24,25],vbs09397:[24,25],vbs09460:[24,25],vbs09466:[24,25],vbs09467:25,vbs09477:25,vbs09482:25,vbs09483:25,vbs16624:24,vbs16625:24,vbs16626:24,vbs16628:24,vbs16630:24,vbs24195:[5,6],vbs24195_cnv_hmm:6,vbs24196:[5,6],vbs24197:[5,6],vbs24198:[5,6],vbs24199:[5,6],vbs24200:6,vbs24201:[5,6],vbs24202:6,vbs24203:6,vbs24213:5,vbs24216:5,vbs24534:5,vbs24535:5,vbs24536:5,vbs24537:5,vbs24539:5,vcf:22,ve:[5,20,24],vector:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,24,25,26,29],veget:29,veri:[20,29],verif:30,verili:29,vernick:29,version:[5,20,22,28,29],versu:21,vertex:30,vet:29,veterinari:29,vgsc:29,via:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,29,30],vial:29,viana:29,vicent:29,victoria:29,vid:20,video:30,view:[6,21,22,30],viewer:29,vihear:26,villag:[21,29],vincent:29,vincenzo:29,virginia:29,virtual:30,visit:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,19,21,23,26,27,29],vm:30,vmf00004:8,vmf00013:[1,11],vmf00014:11,vmf00015:10,vmf00025:[1,11],vmf00028:11,vmf00029:11,vmf00043:[0,5,6],vmf00044:[0,5,6],vmf00045:[0,5,6],vmf00046:11,vmf00047:[1,11],vmf00050:10,vmf00051:10,vmf00052:10,vmf00054:10,vmf00067:[1,10],vmf00088:15,vmf00090:[0,5,6],vmf00094:[0,5,6],vmf00095:[0,5,6],vmf00095_funestus_2rl_phas:6,vmf00095_funestus_cnv_coverage_cal:6,vmf00099:[0,5,6],vmf00101:[0,5,6],vmf00102:15,vmf00106:[1,12],vmf00140:12,vmf00149:[1,12],vmf00160:13,vmf00161:13,vmf00162:13,vmf00164:[1,13],vmf00165:14,vmf00168:14,vmf00173:14,vmf00176:[1,14],vmf00178:14,vmf00185:15,vmf00193:15,vmf00197:15,vmf00202:15,vmf00208:15,vmf00212:15,vmf00218:17,vmf00219:[1,16],vmf00222:17,vmf00227:[2,17],vmf00228:17,vmf00232:17,vmf00235:17,vmf00242:17,vmf00244:9,vmf00246:17,vmf00248:1,vmf00250:9,vmf00252:2,vmf00259:9,vmf00261:3,vo:[0,1,2,3,5,6,8,9,10,11,12,13,14,15,16,17,25],vo_afun_releas:[5,6],vo_afun_release_master_us_central1:5,vo_agam_output:21,vo_agam_releas:[20,21],vo_amin_releas:[24,25],vt:29,vugt:29,w:29,wa:[5,6,20,21,22,24,25,26,29],wageningen:29,wai:[5,20,22,24],waiv:[10,11],wali:29,walkthrough:30,wambua:29,want:[0,5,6,7,20,21,24,25],warn:[5,20],water:29,watsenga:[1,13],watsengan:1,wc1e:29,wdl:22,we:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29,30],web:21,webpag:[0,1,2,3,9,10,11,12,13,14,15,16,17],websit:[1,2,3,5,8,9,10,11,12,13,14,15,16,17,20,21,30],weetman:29,welcom:27,well:[22,29],wellcom:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26,29],were:[1,5,6,7,20,21,22,24,25,26,28,29],west:[0,1,16,22,29],western:29,wet:[24,25],wga:22,wget:[6,21,25],wgs_snp_data:[6,21,25],whatshap:22,whatsoev:22,wheel:[20,24],when:[1,2,3,5,6,20,21,22,24,25,29,30],where:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,28,29],whether:[6,20,21],which:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,26,29,30],white:29,who:[0,7,29],wi:29,wide:[5,6,20,21,28],widespread:26,wild:[7,20,21,22,29],wildlif:29,wilkerson:29,wilkin:29,willem:29,william:29,wim:29,wind:29,window:[5,6,20,21,22,29],winifrida:29,wisconsin:29,within:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29,30],without:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,26,29],wo:5,won:[6,21],wondji:[0,5,6],woodland:29,work:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,26,30],workbench:30,workspac:30,would:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29],wrap:[5,20],wrapper:[5,20,24],wright:29,www:[5,6,21,29,30],x27:[5,20,24],x:[5,6,7,20,21,22,29],xag:22,xarrai:[5,20,24],xavier:29,y:29,yahoo:29,yallal:29,yanfolila:29,yao:29,yawson:[1,10,12,29],year:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,29],yeka:29,yey:29,yield:[22,29],yopougon:29,you:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,28],youden:22,your:[0,5,6,7,20,21,25,30],yourself:[5,20,24],z:[6,21,29],za:[14,17],zambia:[0,1,14,17],zemb:29,zeneti:29,zero:22,zimbabw:9,zip:[6,21],zm:[1,14],zone:29,zoogeograph:29,zoologi:29,zootaxa:29,zymo:29},titles:["Af1.0  (<em>Anopheles funestus</em> Project Phase 1 Data Release)","Af1.1","Af1.2","Af1.3","Af1 API","Af1 cloud data access","Af1 data downloads","Ag3.0 (Ag1000G phase 3)","Ag3.1","Ag3.10","Ag3.2","Ag3.3","Ag3.4","Ag3.5","Ag3.6","Ag3.7","Ag3.8","Ag3.9","Ag3 analysis","Ag3 API","Ag3 cloud data access","Ag3 data downloads","Ag3 sequencing and variant calling methods","Amin1 API","Amin1.0 cloud data access","Amin1.0 data downloads","Amin1.0","MalariaGEN vector data user guide","Release notes","Ag1000G partner studies","Vector Observatory Data Access"],titleterms:{"0":[0,7,24,25,26],"02":28,"03":28,"04":28,"07":28,"09":28,"1":[0,1,8,29,30],"10":9,"11":28,"12":28,"14":28,"15":28,"2":[2,10,29,30],"2021":28,"2022":28,"3":[3,7,11,29,30],"4":[12,30],"5":13,"6":14,"7":15,"8":16,"9":17,"c\u00f4te":29,"public":29,The:29,access:[5,20,24,30],account:30,acknowledg:[22,29],af1:[0,1,2,3,4,5,6],african:29,ag1000g:[7,29],ag3:[7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22],aim:22,align:[21,22,25],all:22,allel:[5,6,20,21,22,24],amin1:[23,24,25,26],an:22,analys:22,analysi:18,ancestri:22,angola:29,anomali:22,anophel:[0,27],api:[4,19,23],appendic:22,ar:30,arabiensi:22,assign:22,authent:30,bam:[21,25],bioko:29,bissau:29,burkina:29,calcul:22,call:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26],cameroon:29,central:29,citat:26,cloud:[5,20,24,30],cnv:[5,6,20,21,22],collect:[6,21],coloni:[22,29],coluzzii:22,commun:27,complex:27,comput:[5,20,24],congo:29,contamin:22,contributor:29,copi:[5,6,20,21,22],count:24,coverag:[5,6,20,21,22],credenti:30,cross:[22,29],d:29,data:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26,27,30],democrat:29,detect:22,discord:[20,21,22],discoveri:22,download:[6,21,25],ensur:30,exampl:[5,20,24],fair:30,faso:29,fastq:21,feedback:[5,6,20,21,24,25],fill:30,filter:[5,6,20,21,22,24],form:30,format:[6,21,25],funestu:[0,27],further:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26],gabon:29,gambia:[22,27,29],genom:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,24,26,27],genotyp:[5,6,20,21,24],ghana:29,googl:30,guid:27,guinea:29,haplotyp:[5,6,20,21,22],have:30,hmm:[5,6,20,21,22],host:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,24,25,26],identifi:22,infer:22,inform:[22,29],input:22,insecticid:22,island:29,ivoir:29,joint:22,kenya:29,larger:[5,20],latest:30,loci:22,make:30,malaria:27,malariagen:27,malariagen_data:30,malawi:29,mali:29,marker:22,mayott:29,metadata:[5,6,20,21,24,25],method:22,minimu:27,model:22,mozambiqu:29,normal:22,note:[27,28],number:[5,6,20,21,22],observatori:[27,30],out:30,outlier:22,packag:30,panel:[6,21],partner:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26,27,29],pass:24,pca:22,phase:[0,7,22],popul:[0,7,22,26],posit:24,project:0,python:30,qc:22,raw:21,read:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,20,21,22,25,26],refer:[6,21,24,29],releas:[0,27,28],replic:22,republ:29,request:30,resist:22,resourc:29,run:[5,20],sampl:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,24,25,26,29],segreg:24,sequenc:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,21,22,25,26],set:[0,1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,29,30],setup:[5,20,24],sex:22,site:[5,6,20,21,22,24],snp:[5,6,20,21,22,24,25],speci:[21,22],specimen:[6,21],state:22,statist:22,step:30,studi:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26,29],subset:[5,20],suggest:[5,6,20,21,24,25],summari:22,sure:30,tanzania:29,technic:22,term:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,26,30],three:22,uganda:29,up:30,us:[0,1,2,3,5,7,8,9,10,11,12,13,14,15,16,17,20,22,26,30],usag:30,user:27,variant:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26],variat:[5,6,20,21],vcf:[6,21,25],vector:[27,30],version:30,via:22,whole:[0,1,2,3,7,8,9,10,11,12,13,14,15,16,17,22,26],wide:22,you:30,zarr:[6,21]}})
\ No newline at end of file
+Search.setIndex({docnames:["af1/af1.0","af1/af1.1","af1/af1.2","af1/af1.3","af1/af1.4","af1/api","af1/cloud","af1/download","ag3/ag3.0","ag3/ag3.1","ag3/ag3.10","ag3/ag3.2","ag3/ag3.3","ag3/ag3.4","ag3/ag3.5","ag3/ag3.6","ag3/ag3.7","ag3/ag3.8","ag3/ag3.9","ag3/analysis","ag3/api","ag3/cloud","ag3/download","ag3/methods","amin1/api","amin1/cloud","amin1/download","amin1/intro","landing-page","release-notes","studies-ag1000g","vobs/vobs-data-access"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":5,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,"sphinxcontrib.bibtex":9,sphinx:56},filenames:["af1/af1.0.ipynb","af1/af1.1.ipynb","af1/af1.2.ipynb","af1/af1.3.ipynb","af1/af1.4.ipynb","af1/api.md","af1/cloud.ipynb","af1/download.ipynb","ag3/ag3.0.ipynb","ag3/ag3.1.ipynb","ag3/ag3.10.ipynb","ag3/ag3.2.ipynb","ag3/ag3.3.ipynb","ag3/ag3.4.ipynb","ag3/ag3.5.ipynb","ag3/ag3.6.ipynb","ag3/ag3.7.ipynb","ag3/ag3.8.ipynb","ag3/ag3.9.ipynb","ag3/analysis.ipynb","ag3/api.md","ag3/cloud.ipynb","ag3/download.ipynb","ag3/methods.md","amin1/api.md","amin1/cloud.ipynb","amin1/download.ipynb","amin1/intro.ipynb","landing-page.md","release-notes.md","studies-ag1000g.md","vobs/vobs-data-access.ipynb"],objects:{},objnames:{},objtypes:{},terms:{"0":[1,6,7,9,10,11,12,13,14,15,16,17,18,21,22,23,28,29,30,31],"00":[6,21,25,30],"000":[23,25],"0000":21,"00000":[6,21],"000000":21,"00000100000":[6,21],"000001651491700000":21,"000001651491800000":21,"00000200000":[6,21],"000002063385700000":6,"000002063385801101":6,"00001":23,"0007664303506418854":22,"00101":6,"0011500862564692352":22,"0013417672992141077":22,"0015322735108216816":22,"0017244682889442423":22,"001915341888527102":22,"002106069308826345":22,"0024904214559386974":22,"00258":[25,26],"00264":[25,26],"0028":30,"0028735632183908046":22,"0035":30,"00384":[25,26],"00393":30,"006":23,"00611":30,"007":25,"008":30,"009":[6,7,25],"01":[6,22,23,30],"010":[6,21,25],"01055":30,"012":[23,25],"01230604":25,"01234":[6,21,25],"0125":21,"012500":21,"014":30,"014316392269148175":22,"01454":25,"01465":25,"01499":25,"01591":25,"016":30,"01604":25,"016488046166529265":22,"0165149170":21,"0165149180":21,"0167":30,"017":30,"018868":21,"019":30,"01949":25,"02":30,"020":[6,21,25],"0206338570":6,"0206338580":6,"022857025604":25,"022857026604":25,"023":25,"023571428571428573":22,"025":[25,27],"026":30,"02604":25,"02631578947368421":22,"027":25,"028":25,"02960":[25,26],"02986":30,"03":[21,26,30],"030928":21,"032":25,"033":[25,30],"0375":21,"037500":21,"03873":26,"04":[22,26],"04070":[25,26],"041":25,"04121":26,"041237":21,"049":30,"05":[21,30],"050":30,"05011":26,"051":25,"05167":26,"055":30,"057":25,"06":[21,26,30],"061":25,"062":25,"0625":21,"06692864":21,"06693":21,"068":25,"0680161":30,"06931525":21,"07":[21,26,30],"076923":21,"07_gamb_2004":21,"08":21,"080":30,"081":[8,23,29],"083":[6,7],"08729639":21,"09":[21,22,30],"093443":30,"094":30,"099":25,"09_colu_2012":21,"09_colu_2014":21,"09_gamb_2012":21,"09_gamb_2014":21,"0_funestus_":7,"0_funestus_3rl_phas":7,"0g":22,"1":[3,4,6,7,8,10,11,12,13,14,15,16,17,18,21,22,23,25,27,28,29],"10":[0,6,7,8,18,21,22,23,25,27,28,30],"100":[6,7,8,21,22,23,25,30],"1000":[8,19,21,22,23],"10000":6,"1000000":[7,22],"1002":12,"1004236":30,"1009253":30,"101":[8,17,21,22,30],"1015":7,"1016":30,"102":[8,21,22,25,27],"102870901":6,"102872101":6,"102872400":6,"102873600":6,"102882608":6,"102882609":6,"102882610":6,"102882611":6,"102882611allel":6,"102882901":6,"102883200":6,"102883201":6,"102883500":6,"102883501":6,"102883511":6,"103":[21,25,30],"10362":30,"1038":30,"103mb":6,"104":[13,21,25,26,27],"1046":30,"105":[21,25],"10506474":21,"1051":21,"10583542":30,"106":[25,27],"107":[25,27],"109":30,"1093":30,"1095":13,"10g":22,"11":[4,6,12,18,21,22,25,26,27,30],"110":[2,21],"1101":[27,30],"1106":6,"111":[21,30],"1111":30,"112":[21,30],"1121":30,"11226723":21,"1125":21,"1126":30,"113":[15,18,21],"113208":21,"11354":30,"1138":[1,11],"114":6,"1140":14,"1150":1,"116":25,"1164":10,"11646":30,"117":17,"1175":26,"1177":[9,11],"1178":[1,12],"1186":30,"1188":[4,10],"119":[6,30],"1190":[1,12,16],"1191":[1,13],"12":[2,6,9,15,17,18,21,22,23,25,26,27,30],"120":[21,25],"1200":23,"1203":30,"12084":30,"121":12,"122":[18,25],"1221":30,"1229":[0,6,7],"122kb":6,"123":21,"1230":[0,1,6,7,17],"1231":[0,6,7,30],"1232":[0,6,7],"1235":[0,6,7],"1236":[0,1,2,3,6,7],"1237":[1,11,16],"1240":[0,6,7],"1242":30,"1244":[1,11,13],"1245":11,"1246":16,"125":[6,21,25,30],"12510902":30,"1253":11,"126":21,"1261":30,"1264":[1,14],"127":21,"1270":[10,14,16,18],"1272":14,"1273":[1,15],"1274":[18,30],"1275":30,"1279":15,"128":21,"1280":[15,18],"1281":[2,16,18],"1288":[1,15,17],"129":21,"12950":21,"13":[0,6,8,16,21,22,23,25,26,27,30],"130":[23,25,30],"1303":30,"13071308130913101311000000":6,"131":17,"1312":6,"1314":17,"1315":[1,17],"1323":18,"13245149":21,"1325":21,"1325arrai":21,"1326":[1,17],"1329":18,"133":[25,30],"1330":[4,10],"1332939":21,"1333":21,"134":[15,21],"1349":30,"135":21,"1354":4,"135gb":6,"136":25,"1365":30,"137":8,"1371":30,"13754":21,"138":3,"14":[6,13,21,25,30],"140":30,"1404":15,"141":[13,21,25],"1415":25,"142":11,"143":30,"144":[18,21,25],"145":14,"146":18,"1470":21,"1470variant":21,"1472":30,"1475":30,"148718":30,"149":[10,30],"15":[6,8,13,17,18,21,23,25,27,30],"150":[23,25,30],"1500":21,"151":22,"15149":21,"153":[17,21,25],"1534":30,"154":21,"155":[25,27],"156":30,"157":14,"158":[6,15],"159":25,"159160161162163000000":21,"15x10x5cm":30,"16":[4,6,9,10,12,16,17,21,23,25,30],"160":[14,21,30],"161":30,"162":21,"163":[12,15,18,21],"1630":18,"164":[10,13,21],"16420701":30,"165":[14,21],"165149160":21,"1651491600000":21,"16514919":21,"16514919coordin":21,"166":[9,15,18,21],"167":[6,13,21],"168":[21,25,30],"16896122":30,"169":[21,30],"16th":4,"17":[6,7,10,17,21,22,30],"170":21,"171":[21,25],"17177993":30,"172":[8,21,25],"173":[10,16,21],"1736":21,"174":[8,21,22],"175":[21,30],"1756":30,"175mb":6,"176":21,"177":2,"178":[15,25],"179":[11,17],"17th":[9,11,12,13,14,15,16,17],"18":[0,1,6,17,18,21,25,30],"180":[10,30],"181":[8,12,21,22],"1817":13,"18187801":30,"182":[15,30],"183":[13,30],"184":21,"18496":21,"185":[8,21,22],"186":12,"188":18,"189":21,"19":[1,6,8,14,17,18,21,23,29,30],"190":[17,21],"192":21,"193":[3,21,22,30],"19303125":30,"194":21,"195":21,"19579":21,"196":[4,21],"1968":30,"197":[6,12,25],"1979":30,"19797":21,"1986":10,"1987":30,"1988":10,"199":21,"1993":[8,30],"1994":8,"1997":30,"1998":[18,30],"1999":30,"1arrai":21,"1gb":6,"1mb":6,"1s":6,"1sa":30,"1tb":6,"2":[1,6,8,12,13,16,17,18,21,23,25,26,28,29],"20":[6,14,15,21,23,25,30],"200":[21,22,23,30],"2000":[2,8,23,30],"2001":[1,2,14],"2002":[2,8,18,30],"2003":[8,18,30],"2004":[1,8,10,18,30],"2005":[1,8,10,18,30],"2006":[1,8,18,30],"2007":[1,8,16,18,30],"2008":[1,10,16,17,30],"2009":[8,10,18,21,30],"201":[15,21],"2010":[1,8,10,18,25,27,30],"2011":[1,8,17,18,23,25,27,30],"2012":[1,8,9,10,16,17,18,21,22,23,30],"2013":[1,8,9,11,12,14,17,18,30],"2014":[0,1,8,9,11,13,14,16,17,18,25,27,30],"2015":[0,1,6,8,9,10,11,13,17,18,23,25,27,30],"2016":[0,1,12,13,14,16,17,23,25,26,27,30],"2017":[0,1,6,7,10,11,12,13,14,15,17,18,23,30],"2018":[0,1,11,12,13,14,15,16,17,18],"2019":[1,14,15,16,17,18,23,26,30],"202":[21,25],"2020":[1,2,4,10,14,15,16,17,18,30],"2021":[1,4,10,15,16,17,18,27,30],"20211101":[21,29],"2022":[1,2,3,4,10,18,22],"2023":[2,3,4],"20231215":6,"2025":[9,11,12,13,14,15,16,17],"2026":[0,1,2,3,4,10,18],"203":[21,22],"204":12,"205":21,"205151":21,"205151coordin":21,"206":21,"206338560":6,"2063385600000":6,"20633859":6,"20633859allel":6,"207":8,"208":[17,21],"209":[21,25],"20c":30,"21":[1,6,10,16,18,21,25,30],"210":30,"2100":21,"2104":[1,17],"212":[18,25],"2125":30,"213":[21,25],"2132":30,"214":1,"215":25,"216":21,"217":30,"21866":21,"219":[21,30],"21mb":6,"22":[0,1,6,8,21,25,30],"2203":[1,17],"2204":17,"2208":30,"221":[21,25],"221variant":21,"222":[21,30],"223":18,"224":21,"225":[21,30],"226":21,"2261":17,"227":[16,21],"228":[21,25],"22857024604":25,"22857027":25,"23":[6,8,9,11,21,22,30],"2304":[4,10],"233":[22,30],"234":[21,25],"235":[12,21,22,30],"236":21,"237":13,"239":[6,21],"24":[6,12,16,17,18,21,23,25,30],"240":[21,25],"24061":30,"243":[17,21],"244":21,"245kb":6,"246":[16,25,30],"24th":10,"25":[6,16,21,25,30],"250":23,"251":6,"252":[10,21,22,25],"252k":22,"253":21,"2546":16,"255":16,"256":[6,21],"257":25,"258551":22,"259":[21,25],"25928":21,"25h":[21,25],"25hdone":[21,25],"25l":[21,25],"26":[6,8,12,17,21,25,27,30],"260":25,"261":30,"262":21,"262144":[6,21],"263":1,"265":[12,18],"268":[11,16],"27":[1,6,8,21,30],"270gb":6,"271":[21,25],"272":30,"273":[16,18,25],"2738":30,"274":[21,30],"2749":30,"276":[16,30],"2779278027812782278300":21,"2784":21,"2784variant":21,"27gb":6,"28":[1,6,8,10,12,13,18,21,22,30],"281":6,"283":[9,30],"28465673":21,"28472728":21,"28473600":21,"28473874":21,"28474576":21,"28475128":21,"28475490":21,"28475996":21,"28477220":21,"28477540":21,"28477710":21,"28477889":21,"28478057":21,"28478272":21,"28478925":21,"28478987":21,"28479181":21,"28479407":21,"28479548":21,"28480166":21,"28480189":21,"28480193":21,"28480335":21,"28480372":21,"28480547":21,"28480585":21,"28483069":21,"28483236":21,"28483253":21,"28483372":21,"28483384":21,"28483442":21,"28483473":21,"28483475":21,"28483675":21,"28484157":21,"28484338":21,"28484518":21,"28485005":21,"28485033":21,"28485380":21,"28486036":21,"28487546":21,"28491215":21,"28491431":21,"28493547":21,"28494017":21,"28494597":21,"28496505":21,"28496700":21,"28496953":21,"28497279":21,"28497740":21,"28499200":21,"28518123":21,"28520016":21,"28522671":21,"28555300":21,"28556726":21,"28563596":21,"287":15,"2875":30,"28795255":21,"288":[6,30],"288b":6,"289":21,"29":[1,6,21,25,30],"290":[8,21,22],"291":30,"2915":30,"292":[6,25],"293":30,"294":[21,25],"295":21,"297":[8,21,22,23,25],"29729829930030100":25,"298":[21,25],"299":[21,25,30],"29th":[0,1,2,3],"2arrai":21,"2c":30,"2coordin":6,"2gb":6,"2kb":6,"2l":[21,22],"2min":21,"2ploidi":21,"2r":[21,22],"2rb":30,"2rj":30,"2rl":[6,7],"2rl_sitefilt":7,"2sampl":[6,21,25],"3":[1,2,6,7,10,13,16,18,21,22,23,25,26,28,29],"30":[6,21,23,25,30],"300":[6,7,8,21,22,23,25],"300000":[6,21,25],"301":[6,21,25],"30141517":25,"301415170008301415186000301415194000":25,"30141518":25,"30141519":25,"30141520":25,"30141520coordin":25,"302":[21,25,27],"302variant":25,"303":[8,21,22],"305":[7,18],"306":25,"30614":6,"30614sampl":6,"3076":21,"3076307730783079308000":21,"3077":21,"3078":21,"3079":21,"3080":21,"3081":21,"3081coordin":21,"3081variant":21,"30km":30,"31":[0,6,8,10,21,22,25,30],"313":[14,25],"3156":30,"31626230":25,"317":2,"31kb":6,"32":[6,8,10,18,21,25,30],"320":[0,6,7,21],"321":21,"3222999974":22,"323":17,"327":[16,17],"329":23,"33":[6,8,17,21,25,30],"3305":30,"334":6,"34":[0,6,25,30],"341":30,"3426":21,"342946":6,"342946sampl":6,"343":6,"3436926":21,"343kb":6,"344":1,"3447950":21,"345":30,"346":25,"34853":21,"35":[6,18,30],"350":30,"3501850":21,"3512200":21,"3518900":21,"3535850":21,"3539300":21,"356":25,"357":25,"3573750":21,"3599050":21,"36":[0,1,6,7,8,11,17,22,25,27,30],"360":30,"3616290":21,"3619":30,"3619000":21,"3639":18,"3639836":21,"364":25,"3654":21,"3668":21,"3668sampl":21,"367":30,"368":21,"36ploidi":6,"37":[0,13,14,21,25,30],"376":25,"379":15,"38":[6,11,18,21,23,25,30],"380":[16,21],"382":14,"384":30,"388":25,"38878":21,"39":[1,6,21,25,27,30],"392":6,"394":6,"394408":30,"395":25,"398":11,"3af":30,"3arrai":21,"3l":[21,22,23],"3r":[6,7,21,22,23],"3r_sitefilt":22,"3rl":[6,7],"3sz":30,"4":[1,6,7,8,10,12,14,16,18,21,22,23,25,26,27,28,30],"40":[0,6,7,21,25,27,30],"400":30,"408":30,"409":21,"40coordin":21,"41":[0,8,17,18,21,22,25,30],"410":30,"411":25,"412mb":6,"413":25,"414":25,"417":30,"41mb":6,"42":[6,10,21,30],"420":[6,7],"421":25,"422":13,"423":30,"4248stdy7308980":[25,26],"4248stdy7308981":[25,26],"4248stdy7308982":[25,26],"4248stdy7308986":[25,26],"4248stdy7308989":[25,26],"4248stdy7308990":26,"4248stdy7308994":26,"4248stdy7308996":26,"4248stdy7308997":26,"4248stdy7918667":25,"4248stdy7918668":25,"4248stdy7918669":25,"4248stdy7918670":25,"4248stdy7918671":25,"4269":30,"428":25,"43":[0,1,6,7,17,30],"437":25,"439":25,"44":[0,4,6,8,21,22,25,30],"442":30,"443":22,"45":[0,6,8,18,21,22,25,30],"450":[25,30],"451":16,"452":25,"453":[1,22,25],"455":30,"46":[8,17,21,25],"461":[25,30],"4625":21,"464":[25,30],"46556":30,"466":4,"467":16,"468":16,"468219":27,"469":30,"47":[6,21,25,27,30],"472":[22,25,30],"476":25,"477":30,"4779799":6,"47803":21,"479":25,"48":[10,30],"480":25,"482":25,"483":[15,30],"484":25,"485":13,"488":[6,7],"49":[0,12,18,30],"494":25,"497":[6,7,30],"49k":22,"4kb":6,"4km":30,"4min":25,"4ploidi":[21,25],"4s":21,"4sampl":6,"5":[6,7,8,9,10,12,15,16,18,21,22,23,25,27,28,30],"50":[0,1,6,7,16,21,22,23,25],"500":30,"501":25,"502":[6,21],"506":30,"507":21,"508":14,"51":[6,9,21],"511":[6,30],"511b":6,"511coordin":6,"512":6,"514":21,"516":30,"52":[16,21,30],"520":[25,30],"52226565":21,"52226566":21,"52226567":21,"52226568":21,"52226568coordin":21,"524":[21,25],"524288":[6,21,25],"529":[25,30],"53":[8,17,21,22,30],"532":21,"53226":30,"533":23,"534":25,"535":30,"536":25,"537":25,"54":[8,14,25],"540gb":6,"544":25,"545":30,"548":[25,27],"5488":6,"549":30,"55":[1,2,3,21,25,30],"550":30,"552":18,"554":25,"55635564556555665567000000":21,"5568":21,"558":30,"56":[21,30],"563":23,"564":18,"565":23,"566038":21,"567":30,"569":25,"57":[6,12,13,21,25],"571":25,"578":25,"58":[18,25],"582":30,"583":30,"586":25,"59":[2,6,17,18,25],"594":[6,25],"595":[25,27],"5kb":6,"5m":[22,30],"5ml":30,"5s":25,"6":[1,6,8,10,11,14,16,17,18,21,22,23,25,26,28,30],"60":[8,14,21,22,25],"600":[6,21],"601":[6,21],"602":[1,25],"604":[25,30],"605":21,"609":30,"61":[6,21,22],"61303692":21,"61306248":21,"61372543":21,"614":21,"61418536":21,"61478226":21,"61478226arrai":21,"61478802":21,"61478802arrai":21,"61514401":21,"61515901":21,"61517400":21,"61517700":21,"61533301":21,"61535700":21,"615385":21,"61544401":21,"61544700":21,"61544701":21,"61545000":21,"61545001":21,"61545105":21,"617":30,"618557":21,"62":[6,10,22],"624":25,"627":25,"629":30,"62mb":22,"63":[13,17,21,22,23,25],"632":21,"633":6,"634050":30,"639":25,"64":[6,8,11,21,30],"641":25,"642":30,"646":25,"647":[9,25],"649":30,"64b":6,"65":[8,13,18,21],"650":30,"651":6,"6516526536546550":6,"65165265365465500":6,"652":6,"653":6,"654":6,"655":[6,25],"65536":[6,21],"656":[0,6,21,30],"656ploidi":6,"659":25,"66":[21,25,27],"660":[10,25],"663":25,"666":11,"667":[25,26,27,30],"668":[6,30],"669":8,"67":[21,25],"674":25,"6768697071000000":6,"678":25,"6785":30,"67gb":6,"68":[6,8,30],"680":30,"683":18,"685":25,"6885930":30,"689":25,"69":[8,13,15,16,21,22,25],"690":30,"693":23,"6am":30,"6pm":30,"7":[1,6,7,8,11,12,17,21,22,23,25,28,30],"70":[17,21,25,30],"700":30,"701":30,"701mb":6,"703":25,"707":25,"708":25,"71":[4,6,8,21,22,25],"710":25,"711":25,"716":30,"717391":21,"719":25,"72":[6,10,18,25],"721":30,"722":25,"725":25,"726":[25,30],"73":[8,9,21,22,25,30],"730":25,"733":[4,25],"7335":21,"735":[25,27],"737":25,"739":17,"74":[8,12,21,22,25],"741":25,"742":[25,30],"743":25,"744":25,"746":25,"747":30,"7475":30,"75":[10,21,25,30],"750":30,"75015":30,"751":30,"7524":21,"755":30,"757":25,"76":[0,6,7,8,12,15,21,22,25],"762":[25,30],"77":[14,21,25,27,30],"774":30,"776":25,"777":30,"779":30,"78":[6,11,21,22,25,30],"784":[8,21,23],"79":[6,30],"79113":6,"79116":6,"79117":6,"79120":6,"79128":6,"79129":6,"79130":6,"79133":6,"79134":6,"79136":6,"792":25,"7ht":30,"7py":30,"8":[0,1,6,7,8,10,16,18,21,22,23,25,28,30],"80":[8,21,22,25,30],"800":[25,30],"80101":6,"80108":30,"803":25,"81":[0,2,6,7,8,21,22,30],"810":30,"817":30,"82":[8,21,25],"820":21,"821":30,"822":25,"82200":6,"823":[25,30],"825":25,"82variant":21,"83":[21,25,30],"83400":6,"83401":6,"838":25,"83mb":6,"84":[6,8,21],"840":30,"843":25,"844":30,"849":[25,30],"85":[6,14,16,21,25],"851":6,"855":25,"8567335243553008":22,"857":25,"859":6,"86":[6,8,21,22,25],"860":30,"861":30,"864":25,"86400":6,"8658536585365854":22,"868":30,"8686288585786073":22,"87":[8,21,25],"870":30,"870157819225251":22,"873":25,"875":25,"88":[6,13,21,25],"880":30,"884":21,"89":[21,30],"890":30,"891":30,"8925":21,"897":25,"898":[25,30],"8coordin":6,"9":[1,6,7,8,10,11,13,16,17,21,23,25,27,28,30,31],"90":[6,8,11,13,21,23,25,30],"900":[6,21,30],"90036":30,"91":[6,21],"910":25,"912":30,"913":[25,30],"9157060518731989":22,"916":25,"917":30,"918":25,"919":21,"91m":22,"92":[6,15,21,25,27],"9203":30,"922":25,"9247311827956989":22,"928":25,"93":[8,21],"933":30,"938":25,"94":[1,10,13,15,17,21,25],"94080":30,"941":25,"941923":25,"943":25,"9459":21,"9459coordin":21,"94kb":6,"95":[1,16,21,23,30],"952":[6,7],"957":30,"96":[10,21],"966":25,"969":21,"97":[6,8,16,21,22,30],"972":30,"972083035075161":22,"9735973597359736":22,"974":25,"975":17,"9750830564784053":22,"977":25,"9777411376751854":22,"979":21,"98":[6,21],"9801652892561984":22,"9810074318744839":22,"982":[25,26,27],"984297520661157":22,"9875930521091811":22,"99":[6,8,18,21],"991":30,"995":[25,27],"995f":30,"996":25,"9985":21,"9th":18,"\u00e0":30,"\u00e8":30,"\u00e9":30,"amab\u00e9lia":30,"boolean":[6,21,25],"byte":[6,21,25],"case":[1,2,3,4,6,7,22,30],"catch":30,"class":[6,21,23,25],"default":[6,7,31],"diabat\u00e9":30,"direc\u00e7\u00e3o":30,"djogb\u00e9nou":30,"do":[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,30,31],"end\u00e9mi":30,"final":[23,30],"float":30,"fr\u00e9d\u00e9ric":30,"function":[5,6,7,20,21,23,24],"guina\u00e9":30,"import":[6,21,25],"jo\u00e3o":30,"k\u00e9toh":30,"long":[6,21,22],"m\u00fcller":30,"mal\u00e1ria":30,"mich\u00e8l":30,"minist\u00e9rio":30,"minista\u00e9rio":30,"new":[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27,29,30,31],"null":23,"p\u00e5lsson":30,"p\u00fablica":30,"pa\u00fablica":30,"pag\u00e8":30,"public":[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27,31],"regi\u00e3o":30,"resist\u00eancia":30,"return":[6,21],"ros\u00e1rio":30,"s\u00e6b\u00f8":30,"sa\u00fad":30,"saa\u00fad":30,"sangar\u00e9":30,"sant\u00e9":30,"short":[0,8,30],"static":[6,7],"tiassal\u00e9":30,"true":[1,2,3,4,6,21,23,25,30],"universit\u00e0":30,"while":30,"yaound\u00e9":30,A:[6,7,8,21,22,23,25,26,29,30],As:[6,21],At:30,For:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,30],IN:30,If:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,29,31],In:[0,6,8,21,30],It:30,No:[23,25],Not:[6,21,23,25],On:[6,21],One:23,The:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,27,29,31],Then:[7,22],There:[6,7,21,22,30],These:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30,31],To:[1,2,3,4,6,7,19,21,22,23,25,26,28,31],With:30,_:22,_funestus_:7,_phase:[7,22],ab0085:22,ab0086:22,ab0087:22,ab0088:22,ab0089:22,ab0090:22,ab0091:22,ab0092:22,ab0094:22,abaga:30,abdisalan:30,abdoul:30,abdoulay:30,abdrahaman:30,abidjan:30,abl:[6,21,23],about:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,30],abov:[0,1,2,3,4,6,10,11,12,13,14,15,16,17,18,21,22,23,26],abrahan:30,absenc:[6,21,30],absolut:30,abyzov:23,ac0398:30,ac:[0,6,7,21,22,25,26,30],ac_pass:25,academ:31,acc:21,access:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22,23,24,26,27,28],accommod:23,accord:[23,30],account:23,accra:30,ace1:[21,23,30],ace1_del1:21,ace1_del2:21,ace1_del3:21,ace1_del4:21,ace1_dup0:21,ace1_dup1:21,ace1_dup2:21,acet:30,acetylcholin:21,acetylcholinesteras:30,acid:[21,30],acoust:23,across:[0,6,7,18,21,22,23,30,31],activ:30,actual:[6,21,25],ad0494:21,ad0495:21,ad0496:21,ad0497:21,ad0498:21,ad:[1,2,3,4,6,7,22,23,29,30],adam:30,adapt:[1,2,3,4,6,9,10,11,12,13,14,15,16,17,18,21,23,30],add:[6,7,21,22,25,26],addit:[8,30],addition:22,address:31,adher:31,adiamoh:30,admin1_iso:[6,21],admin1_nam:[6,21],admin1_year:21,admin2_nam:[6,21],adok:30,adopt:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],adult:30,advis:31,aerosol:30,aestiv:[9,11],af1:28,af1_sc:6,af:[1,7],affect:23,africa:[0,1,10,15,17,18,30],african:[0,1,8,11,13,14,16,18,19,29],afriqu:30,afrotrop:30,after:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27,30],ag1000g:[1,19,21,22,23,28],ag3:[1,28,29],ag3_:22,ag3_gamb_colu_arab_3l_phas:22,ag:22,agamp4:23,agap001096:21,agap001097:21,agap001098:21,agap004674:21,agap004675:21,agap004676:21,agap013094:21,aggfunc:25,ago:21,agreement:31,agricultur:30,ah32:7,ai:31,aim:[21,22],aim_20200422:21,aim_speci:[21,22],aim_species_fraction_arab:22,aim_species_fraction_colu:22,aim_species_fraction_colu_no2l:22,aim_species_gambcolu_arabiensi:22,aim_species_gambiae_coluzzii:22,ajtmh:30,akron:30,al:[23,27,30],alcohol:30,alert:30,alessandra:30,alessandro:30,alexand:30,alexandra:30,ali:30,align:[0,6,7,8,21,25,27],alignments_bam:26,alina:30,alinun:30,aliv:30,all:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,30,31],allel:30,allele_consist:22,allelecountsarrai:25,allelism_count:25,alli:30,allison:30,alloc:31,allow:[0,6,7,21,22,23,25,31],almost:30,along:[23,30],alpha:23,alphabet:8,alreadi:[22,26],also:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30],alt:[7,22],altern:[6,7,21,22,23,25,26,31],although:[1,2,3,4,6,9,10,11,12,13,14,15,16,17,18,21,30],alwai:[6,7,21,22,25],am:30,amabelia:30,amad:30,ambigu:23,ambros:30,amenga:[1,12,16],american:30,amfaal:30,amharicu:30,amin1:[28,29],among:[23,30],amount:22,amp:21,amplic:23,amplif:[6,21],amplifi:23,an:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,29,30,31],analys:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,25,26,27,29,30],analysi:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,26,27,28,29,30],anatol:30,ancestri:22,angela:30,angola:[8,18,21],ani:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,29,30,31],anim:30,anitha:30,ann:30,annot:[21,23],annual:30,anophel:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,27,29,30],anophelin:30,anophelina:30,anospp:[0,1,17,18],anoth:31,antananarivo:30,antao:30,antula:30,ao:[8,21,22,30],ao_:22,ao_cnv_discordant_read_cal:22,ao_cnv_hmm:22,ao_gamb_colu_2l_phas:22,ao_gamb_colu_cnv_coverage_cal:22,api:[6,19,21,28],appar:[23,30],appear:30,appendix:23,appli:[6,21,22,23,25],applic:[22,31],approach:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23],appropri:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23],approxim:[6,7,21,22,23,25,26,30],apr:[25,26],april:[0,1,2,3,18,30],ar0001:[21,22],ar0002:[21,22],ar0004:[21,22],ar0006:[21,22],ar0007:[21,22],ar0008:22,ar0009:22,ar0010:22,ar0011:22,ar0047:[21,22],ar0049:[21,22],ar0051:[21,22],ar0061:[21,22],ar0072:22,ar0078:[21,22],ar0080:22,ar0084:22,ar0097:22,ar:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,27,30],arab:[21,22,23],arabiensi:[8,9,10,11,12,13,14,15,16,17,18,21,22,29,30],archiv:[0,7,8,22],area:[23,30],arez:30,arid:30,arj:30,arlet:30,arm:[6,7,21,22,23],around:[7,22,23,30],arrai:[6,21,25],articl:30,ascertain:30,asciitre:[21,25],ascot:30,asia:27,ask:31,aspir:30,assai:30,assess:[18,30],assign:[21,22,25,26,30],associ:[7,18,22,23,26,30,31],assum:[6,7,21,22,25,26],attribut:[6,21,25],august:[4,30],aurelio:30,auroc:23,austin:[22,30],auth:31,authent:[6,7,21,22,25,26],automat:31,autosom:[6,21,23,30],avail:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,29,31],avaradoha:30,averag:23,avoid:23,awai:30,await:22,awolola:30,axi:25,ayala:[0,1,6,7,17,30],aydi:[1,17],b5:30,b:[6,7,8,21,22,23,25,26,30],back:[6,21,23,25],badzer:30,bag:30,balanc:23,baltimor:30,bam:7,bamako:30,bana:[22,30],banambani:30,bancoumana:30,bangui:30,banjul:30,bank:30,bap:30,barri:30,barron:16,base:[6,7,16,21,22,23,25,26,30],baselin:0,basi:30,basiliana:30,bass:30,bcftool:[7,22],beavogui:30,becaus:[6,7,21,22,23,25,31],becki:30,been:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,25,27,29,30],befor:[0,1,2,3,4,9,10,11,12,13,14,15,16,17,18,23,30],being:23,bejon:30,belong:[7,21,22],below:[0,6,7,8,21,22,23,25,28,30],bendiocarb:30,beneath:23,benedict:30,benefit:31,beniamino:30,benin:[0,1,11,16,18,30],benjamin:30,bennett:30,berg:30,bergei:18,berkshir:30,besanski:30,best:[6,21,23,25,31],better:23,between:[6,9,18,21,23,30],bf2:22,bf3:22,bf:[8,17,21,22,30],bia:30,biallel:[6,21,22,23,25],bias:23,bika72:30,bilali:30,bincount:25,binomi:23,bio:30,bioassai:30,biol:30,biolog:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30],biologi:30,bionom:30,biorxiv:27,bioscienc:30,birom:30,bissau:[8,18,23],bite:30,bj:[1,11,16],bl0047:21,bl0048:21,bl0049:21,bl0050:21,bl0055:21,blacksburg:30,blantyr:30,block:23,blood:30,bloomsburi:30,bmc:30,board:[6,7,21,22,25],boas:30,bobo:30,bolognetti:30,bool:[6,21,25],booldask:[6,21,25],boolfals:21,border:30,borongo:30,bortel:30,both:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27,30,31],botha:30,boto:7,bott:30,boubacar:30,bov:30,box:30,bp:[6,7,21,22,23,30],bradlei:30,bradwhit:30,brama:30,brandi:[25,26,27],brandyc:27,breakdown:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,30],breakpoint:[6,7,21,22,23,30],breed:30,bretz:30,brian:30,briefli:23,broad:23,broader:23,brogdon:30,broken:8,brows:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27],browser:[22,30],bryan:30,bucket:[6,7,21,22,25,26],bug:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,25,27,29],build:[0,1,2,3,4,7,9,10,11,12,13,14,15,16,17,18,21,22,25],burkina:[2,8,10,13,16,17,21,22],burt:[22,30],buya:30,bwa:23,byaruhanga:30,c:[6,8,21,22,23,25,30],ca:30,cabo:6,caccon:30,cach:6,calcul:[6,21],calibr:23,california:30,call:[28,29],call_ad:[6,21,25],call_cn:[6,21],call_genotyp:[6,21,25],call_genotype_mask:[6,21,25],call_gq:[6,21,25],call_mq:[6,21,25],call_normcov:[6,21],call_rawcov:[6,21],calldata:[7,22],callset:22,calvin:30,calzetta:30,cambodia:[25,26,27,29],cambridg:30,came:[27,30],cameroon:[0,2,8,10,16,18],campo:[18,30],can:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,27,30,31],cani:30,cano:30,canon:30,cap:23,cape:30,capit:30,captur:30,caputo:30,carbam:30,carcass:30,carlo:30,carlsbad:30,carnoi:30,carolin:30,carrara:30,carri:[0,8,21,23,27,30],cat:[7,22],catalog:[7,22,26],catchment:30,caught:[8,21,22,23,30],cb10:30,cb:[25,26],cd:[0,1,6,7,8,14,21,22,30],cdc:30,cell:30,cenci:30,center:[27,30],centr:[23,30],central1:6,central:[0,1,8,17],centrifug:30,certain:[7,22],cf:[0,6,7,8,21,22,30],chabi:30,chain:[21,30],chamkar:[25,27],chang:[1,2,3,4,7,9,10,11,12,13,14,15,16,17,18,22,23,26],character:[2,16,23,30],characteris:30,charif:30,charl:30,charlwood:30,chean:[25,27],check:[30,31],cheick:30,chichiri:30,chickhwawa:30,chikhwawa:30,chipeta:30,chloroform:30,choi:30,choos:[6,21,23,25],chosen:[6,21,25],chri:30,christel:30,christian:30,christoph:[2,16,18,30],christophid:30,chromosom:[6,7,21,22,23,30],chunk:[6,21,25],chunksiz:[6,21,25],ci:[8,11,15,21,22,30],cincinnati:30,circumst:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],cite:27,citi:[23,30],clarkson:30,classif:23,classifi:23,clear:[23,30],clement:30,cli:31,click:[6,21,25],client:6,climat:30,clinic:30,clobber:[7,22,26],closer:[6,21,25],cloud:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,18,22,26,27,28],cluster:[6,7,21,22,23,30],cm:[2,8,16,18,21,22,30],cn:[6,21,23],cn_mode:21,cn_mode_count:21,cnm:27,cnr:30,cnrfp:30,cnv:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,29],cnv_coverage_cal:[6,21],cnv_discordant_read_cal:21,cnv_hmm:[6,21],cnv_type:21,co:30,coast:30,coastal:30,cocoa:30,code:[6,7,8,21,22,25,26],coetze:30,coffinet:30,cog:[7,22,26],cohort:[6,7,8,21,22,23,25,26,29],cohort_admin1_month:[6,21],cohort_admin1_quart:6,cohort_admin1_year:[6,21],cohort_admin2_month:[6,21],cohort_admin2_quart:6,cohort_admin2_year:[6,21],cohort_queri:[6,21],coil:31,colab:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,25,27,31],colinc:30,collabor:[0,6,7,8,9,21,22,27,30],collect:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,23,25,26,27,30],colleg:30,collin:30,column:[6,7,21,22,25,26,30],coluzzi:30,coluzzii:[8,9,10,11,12,13,15,16,17,18,21,22,29,30],com:[21,22,26,30],combani:30,combin:23,come:0,command:[7,22,26,31],commerci:30,common:30,commonli:30,commun:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,19,21,30,31],comoro:18,comparison:23,compat:[7,22,26],complement:23,complementari:23,complet:[6,7,21,22,23,25,30],complex:[8,10,30],complic:23,compon:23,composit:23,comprehens:30,compress:25,compris:[23,27,30],comput:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,18,22,23,26,27,30,31],computation:23,conakri:30,concentr:23,concord:23,conda:25,condit:30,conduct:30,confid:23,config:[6,7,21,25],configur:31,confirm:23,congo:[0,1,8,14],connect:[18,22,30],conserv:23,consid:23,consist:[23,30],consortium:[0,8,30],constant:[11,23,30],construct:[21,22,23,30],contact:[0,6,21,31],contain:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,30],contemporari:30,content:[7,22,23],context:27,contig:[6,7,21,22,25],contigu:[6,7,21,22,23],continu:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27,31],contr:30,contrast:30,contribut:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,30],contributor:[6,7,21,22,25,26],control:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27,30],conveni:[6,7,8,21,22,25],convent:30,convert:[6,21],conwai:30,coordin:[6,8,21,25,27,30],cooseman:30,copi:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27,29],core:[6,21],correctli:31,correspond:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25],correspondingli:30,correwyn:30,cost:31,costa:30,costantini:30,cote:[8,11,15],cotteaux:30,could:[6,7,21,22,23,25,26,31],couldn:21,coulibali:30,council:30,count:[6,21,23],count_allel:[6,21,25],count_nonzero:[6,21,25],counti:30,countri:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,29,30],country_iso:21,coupl:30,cours:[8,19,30],covari:23,cover:[23,30],coverag:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27,30],coverage_cal:[7,22],cp:[7,22],craft:23,craig:30,crawford:16,creat:[6,7,21,22,23,25],cromb:30,cropland:30,cross:[8,21],crosses_stat:22,csv:[7,22,26],ctab:[27,30],cuamba:30,cultiv:30,cup:30,curat:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27],current:[8,31],curv:23,cut:[7,22,26],cutoff:[6,7,23],cx:22,cyhalothrin:30,cyp6:30,cyp6aa1:23,cyp6aa:21,cyp6aap_dup0:21,cyp6aap_dup10:21,cyp6aap_dup11:21,cyp6aap_dup12:21,cyp6aap_dup13:21,cyp6aap_dup14:21,cyp6aap_dup15:21,cyp6aap_dup16:21,cyp6aap_dup17:21,cyp6aap_dup18:21,cyp6aap_dup19:21,cyp6aap_dup1:21,cyp6aap_dup1a:21,cyp6aap_dup1b:21,cyp6aap_dup20:21,cyp6aap_dup21:21,cyp6aap_dup22:21,cyp6aap_dup23:21,cyp6aap_dup24:21,cyp6aap_dup25:21,cyp6aap_dup26:21,cyp6aap_dup27:21,cyp6aap_dup28:21,cyp6aap_dup29:21,cyp6aap_dup2:21,cyp6aap_dup30:21,cyp6aap_dup3:21,cyp6aap_dup4:21,cyp6aap_dup5:21,cyp6aap_dup6:21,cyp6aap_dup7:21,cyp6aap_dup8:21,cyp6aap_dup9:21,cyp6m2:23,cyp6m4:23,cyp6p2:23,cyp6p:21,cyp6z1:23,cyp6z3:23,cyp9k1:23,cytogenet:30,d:[7,8,11,15,22,26],da:[6,21,25,27,30],dadzi:[0,6,7,30],dai:30,daiguen:30,daili:30,damari:30,dame:30,damox:21,danica:30,daniel:30,dar:30,dask:[6,21,25],data:[5,19,20,23,24,29,30],datafram:[6,21,25],dataset:[6,21,22,23,25,27],datasetdimens:[6,21,25],date:[1,2,3,4,6,7,21,22,25,26],dave:30,davi:30,david:30,dayanandan:30,daytim:30,ddt:30,de:[23,30],dead:30,decemb:30,decidu:30,decis:[6,7,23],declin:30,deco:30,deep:30,defin:[6,21],degrad:30,del:21,delet:[6,21,29,31],delgado:6,delimit:[7,22],della:30,dellatorr:30,deltamethrin:30,democrat:[0,1,8,14],den:30,deni:30,dens:30,dentistri:30,deokari:30,depart:30,depend:[0,6,7,8,21,22],deposit:30,depth:[19,21,23],deriv:[6,7,21,22,23],describ:[8,23,30],descript:23,desicc:30,design:[21,22,23],desir:30,despit:18,dessic:27,detail:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,18,22,23,29,30,31],detect:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30,31],determin:[6,7,21,22,23,25,30],develop:[19,23,30],df_gene_cnv_freq:21,df_sampl:[6,21,25],df_sample_set:[6,21],df_samples_phas:[6,21],df_summari:25,di:30,dia:30,diabat:30,diagnost:[1,6,11,13,16,21,23,25,30],diann:30,diatta:30,did:[23,30],didier:30,diego:30,dieldrin:30,differ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,26,30],differenti:[22,30],diggl:30,dim:25,dimabi:[6,7],dimens:[6,21,25],dimension:[6,21,25],dimitra:30,dini:30,dioulasso:30,dip:30,dipartimento:30,diploid:[6,21,23],direct:[22,30],directli:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,30],directori:[7,22,26],disabl:7,disconnect:31,discord:29,discordant_read_cal:22,discuss:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27],diseas:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30],disk:22,displai:23,dissect:30,distanc:23,distinct:[27,30],distribut:[23,30],district:[1,12,16,30],diverg:27,divers:[0,1,12,14,15,16,18,27,30],divid:23,djibril:30,djogben:[1,11,16],dna:[6,8,21,23,27,30],dnaeasi:30,dnazol:30,dneasi:30,doc:[5,6,20,21,24],document:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,24,25,26,27,31],doe:30,doi:[27,30],domin:30,don:30,done:[7,30],donnelli:[1,4,15,17,21,30],doreen:30,dorsei:30,douala:30,doubt:30,doumbia:30,douna:30,down:[8,23],download:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,25,27,28,29],dr:0,drakelei:30,drc:30,dri:30,drive:[18,30],druri:30,dry:[25,26,30],ds_cnv:[6,21],ds_cnv_dr:21,ds_gene_cnv:21,ds_hap:[6,21],ds_haps_cohort:[6,21],ds_hmm:[6,21],ds_snp:[6,21,25],ds_snps_funestu:6,ds_snps_gambia:21,dt_20200416:[6,7,21,22],dtype:[6,21,25],due:[6,21,23],dup0:21,duplic:[23,30],dure:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23,30],durham:30,dwell:30,dynam:30,e1004236:30,e1009253:30,e:[6,7,8,21,22,23,25,30,31],each:[0,1,2,3,4,6,7,8,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30,31],earli:[25,26,30],easi:[22,30],easili:[7,22],east:[23,30],eastern:30,ebi:22,eck:30,eclos:30,eco:[2,16,30],ecol:30,ecolog:[1,12,16,30],edi:30,edit:[7,30],edu:30,educ:31,edward:30,effect:30,effici:[6,7,21,22,31],effort:30,egg:30,egyir:30,eight:30,either:[7,21,22,23,27],elev:[6,7,21,22],elien:30,elig:23,elisa:30,elissa:30,elong:21,em:30,email:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,31],embargo:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,31],emerg:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30],emerson:30,emidi:30,emili:30,emiss:23,empir:23,employ:31,emrich:30,en:30,ena:[0,7,8,22],ena_align:22,ena_analysi:22,ena_run:22,end:[6,21,23],endem:[1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,30],engin:[18,23],enhanc:0,ensur:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,27],enter:23,entomol:30,entomolog:[27,30],environ:30,environment:[18,30],enzym:30,epidem:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30],epidemiolog:[2,14,16,28],epopa:30,eppendorf:30,equal:23,equatori:[8,18,30],eric:30,err323844:22,err328585:22,err328597:22,err343468:22,err343636:22,err343648:22,err347035:22,err347047:22,err352136:22,errat:23,error:[23,30],erz1695275:22,erz1695276:22,erz1695277:22,erz1695278:22,erz1695279:22,erz1695280:22,erz1695281:22,erz1695282:22,erz1695283:22,es:30,essandoh:30,establish:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30],estim:[23,30],et:[23,27,30],eta:22,etc:23,etego:[1,12,16],ethanol:30,ethic:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],ethiopia:[10,14,18],ethiopian:30,etouna:30,european:[0,7,8,22],ev:30,eval:[6,21,25],evalu:[0,15,16,17,23],even:[7,23],event:23,evergreen:30,everi:[6,21,30],everyon:31,evid:23,evol:30,evolut:8,examin:23,exampl:[7,19,22,26,30],except:[21,23],excess:31,exclam:[7,22,26],exclud:[6,7,21,22,23,25],expect:[0,23],experi:7,experiment:[6,21,25],expertis:0,expir:[0,1,2,3,4,9,10,11,12,13,14,15,16,17,18],expiri:0,explor:[6,7,19,21,23,25],extens:[10,30],extract:[27,30],extrem:[23,30],f1:[7,22,26],f5hmz4:21,f:[6,7,21,22,25,30],fabrigar:30,facet:19,facil:23,factor:23,faculti:30,fail:[23,30],falciparum:30,fale:30,fals:[6,21,25],falsearrai:21,falsexarrai:21,famili:30,fanello:30,fanni:30,fanzana:30,far:[23,30],farafenni:30,faranah:30,farm:30,farmland:30,faso:[2,8,10,13,16,17,21,22],faster:[6,21,25],fastq:7,father:30,fatti:21,feasibl:23,feb:[25,26],februari:30,fed:30,feel:[6,21],fell:23,femal:[6,21,23,30],fenitrothion:30,few:[7,22,26,30],fewer:23,field:[6,18,26,27,30],file:[7,22,23,26],fill_valu:25,filter_pass:[6,21,25],find:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,22,25,27,30,31],fine:30,finnerti:30,first:[0,1,6,7,14,21,22,23,25,26,30],fish:30,fit:[6,21,23],five:[23,30],fix:[29,30],flag:[1,2,3,4,6,7],flat:30,float320:21,float32:[6,21,25],float32dask:[6,21,25],flood:30,floor:30,florenc:30,flow:[6,15,21,30],focu:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],focus:[19,23],fofana:30,fold:23,folder:[7,22,26],follow:[6,7,8,11,12,21,22,23,25,26,27,30,31],fondazion:30,fontain:10,fontenil:30,fontenillei:[16,17],food:30,forest:30,form:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,21,30],format:30,fort:[0,30],forum:26,fots:30,fouet:30,found:[0,1,2,3,4,6,9,10,11,12,13,14,15,16,17,18,21,22,25,30,31],four:[2,16,23,30],fourth:30,fr:[8,21,22,30],fraction:23,fragment:[23,30],franc:30,francisco:30,franck:30,frank:30,franklin:30,freder:30,free:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,25,27,31],freeli:31,frequenc:[21,23,30],from:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,27,29,30,31],frq_bf:21,ftp:[7,22],full:[1,23],funestu:[1,2,3,4,5,6,7,15,30],funestusxarrai:6,further:[6,7,21,22,23,25,30],furvela:30,futur:[1,2,3,4,6,23,31],g3:30,g:[6,7,8,21,22,23,25,30],ga:[0,1,6,7,8,17,18,21,22,30],gaardian:[1,11,13,16],gabakoro:30,gabon:[0,1,8,16,17,18],gabu:30,gado:30,gamb_colu:[21,22,23],gamb_colu_arab:[6,21,22,23],gambcolu:22,gambia:[1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,24,29],gamez:30,gap:15,gatk:23,gaussian:23,gaussianhmm:23,gb:[7,21,22,25],gbadolit:30,gbullung:[6,7],gc:[6,7,21,22,23,25,26,27,31],gcloud:31,gcx1:[8,10,14,18,21],gcx2:[8,14,18,21],gcx3:[8,21],gcx4:[16,17],gel:[27,30],gender:[6,7,21,22,25],gene:[6,15,18,21,23,30],gene_cnv:21,gene_cnv_frequ:21,gene_contig:21,gene_descript:21,gene_end:21,gene_id:21,gene_nam:21,gene_start:21,gene_strand:21,gene_window:21,gener:[1,2,3,4,6,7,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,30],genet:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,23,25,26,27,30],genom:[6,7,19,21,22,29,30,31],genome_sequ:25,genotyp:[23,30],genotypedaskarrai:[6,21,25],gentil:30,gentra:30,geoff:30,geograph:30,georg:30,get:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,28,31],gh01:[6,7],gh02:[6,7],gh03:[6,7],gh04:[6,7],gh05:[6,7],gh06:7,gh07:7,gh08:7,gh09:7,gh:[0,1,6,7,8,11,12,13,16,21,22,30],ghana:[0,1,6,7,8,11,12,13,16],ghtm:30,gib:6,gilbert:30,gilli:30,github:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27],give:[6,7,21,22,25,26],given:[6,7,8,21,22,23,25,26,30],glacial:30,global:[0,30],globe:31,glucos:30,gm:[8,14,18,21,22,23,30],gmail:[30,31],gn:[4,8,10,21,22,30],godefroi:30,godfrai:30,goff:30,gome:30,googl:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27],googleapi:[22,26],gov:30,govend:30,gowelo:30,gp:27,gprmac2:21,gq:[7,8,21,22,23,30],gr:30,gradient:30,gradual:30,grant:[30,31],graph:6,grassland:30,grau:30,gravid:30,greater:[6,21,23],greenhous:30,ground:30,group:[23,30],groupbi:[6,21],grove:30,grow:30,gs:[6,7,21,22,26],gste3:23,gstu4:23,gsutil:[7,22,26,31],gt:[6,21,25],gt_cohort:[6,21,25],gtd:25,guel:30,gui:30,guid:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,18,22,23,26,27],guillaum:30,guindo:30,guinea:[4,8,10,16,18,23],gupanarigu:[6,7],gw:[8,21,22,30],gz:[7,22,26],gzip:22,h:30,ha:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,29],had:23,half:[23,30],hamdalai:30,hamlet:30,han:30,hand:23,handl:[23,30],haplotyp:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,29],haplotypedaskarrai:[6,21],hard:[6,7],harold:30,harvard:23,hatch:30,have:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,29,30],hdl:30,hdy:30,head:[6,7,21,22,26],health:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30,31],held:23,help:[1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,31],henc:22,henk:30,henri:30,here:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,25,26,31],hereaft:23,hered:30,het:23,heterogen:[14,30],heterozyg:23,heterozygos:22,heterozygot:23,hi_:22,hidden:23,hierarchi:[7,22],high:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,27,30],higher:31,highest:[23,30],highland:30,highli:23,higien:30,hilari:30,hill:30,hinxton:30,hiseq:23,hmmlearn:23,hof:30,hold:[7,22],home:[7,22,26],hope:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27],hopefulli:[0,8],hour:30,hous:30,how:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,25,26,27],howel:30,howev:31,ht:[6,21],ht_cohort:[6,21],http:[6,7,22,26,27,30,31],hugh:30,human:[18,30],humid:30,hundr:[6,21],hung:30,hunt:30,hut:30,hutchinson:30,hyacinth:30,hybrid:30,hyg:30,hygien:30,hyperendem:30,hyperparamet:23,i:[6,21,23,25,30,31],ibrahima:30,icer:9,icon:[6,21,25],id:[6,21,26],ident:30,identif:30,identifi:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,30],ig:30,igor:30,ihmt:30,ilboudo:30,illo:30,illumina:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27],illustr:[6,21,25],immedi:30,immo:30,immunolog:30,imp:30,impact:[1,15,23],imperi:30,implement:23,implic:[1,14,15,18],improv:30,inc:30,incipi:30,includ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,29,30,31],inclus:23,incorrect:29,increas:[21,23,30,31],increment:23,indel:23,indelrealign:23,independ:[8,23,30],index:[6,7,21,22,25,26],indic:[6,21,23,25,30],individu:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30],indoor:30,infect:[1,12,30],infecti:30,infer:[6,7,21,22],infett:30,inform:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,31],informat:23,inhabit:30,inhamban:30,inher:30,inherit:[6,21,23],inhibitor:21,initi:[23,30],inocul:30,insect:30,insectari:30,insecticid:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,21,22,30],insecticida:30,insert:23,insid:[0,30],inspect:[7,22,23,26],instal:[0,6,21,25,31],instanti:6,instar:30,institut:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,18,22,23,26,27,30],instituto:30,int16:[6,21,25],int16dask:[6,21,25],int32:[6,21,25],int32dask:[6,21,25],int6423:21,int643426:21,int649985:21,int64:[6,21],int82:21,int8:[6,21,25],int8dask:[6,21,25],integ:[6,21,25],integr:[30,31],intend:[7,22,26],intens:30,interact:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,25,27],interest:[6,7,21,22,23,25],intermedi:[21,22,23,30],intermediate_arabiensis_gambia:21,intermediate_gambiae_coluzzii:21,intern:[9,30],interpret:[19,21],intersect:23,interspers:30,interv:23,intervent:[1,15,30],introduc:30,introduct:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,21,22,27],introgress:[10,23,30],invari:25,invers:[23,30],investig:[1,14,15,23],invitrogen:30,involv:[6,8,21,23,30],iowa:6,iran:30,ird:30,irrig:30,irss:30,is_segreg:[6,21,25],isel:[6,21],island:18,isol:30,issu:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,21,22,27,31],issue33725:7,istituto:30,itali:30,italia:30,iter:23,its:[23,30],ivoir:[8,11,15],j:30,jaenson:30,jaim:30,jame:30,jan:[25,26],janet:30,januari:30,jarjav:30,jawara:30,jean:30,jenkin:30,jinja:30,joachim:30,joao:21,johannesburg:30,john:30,johnson:30,jointli:19,jone:30,jorg:30,joseph:30,journal:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30],jovin:30,jpinto:30,jubil:30,jul:[25,26],juli:30,julia:30,juliana:30,jun:23,june:[10,30],junqueira:30,just:[7,8,22],k2:30,k4:30,k6:30,k:[21,25,30],kaaya:30,kababoug:30,kabagh:30,kabr:30,kabula:[16,30],kajo:[1,17],kalataba:30,kamali:30,kamau:18,kamdem:30,kamija:30,kampala:30,kamya:30,kanungu:30,kardo:30,karyotyp:30,kassena:[1,12,16],kavish:30,kayondo:[1,17],kazemb:30,kb663610:25,kb663611:25,kb663622:25,kb663633:25,kb663644:25,kb663655:25,kb663666:25,kb663677:25,kb663688:25,kb663699:25,kb663710:25,kb663721:25,kb663722:25,kb663733:25,kb663744:25,kb663755:25,kb663766:25,kb663777:25,kb663788:25,kb663799:25,kb663810:25,kb663821:25,kb663832:25,kb663833:25,kb663844:25,kb663855:25,kb663866:25,kb663877:25,kb663888:25,kb663899:25,kb663910:25,kb663921:25,kb663932:25,kb663943:25,kb663955:25,kb664054:25,kb664165:25,kb664255:25,kb664266:25,kb664277:25,kb:[21,22,25],kdr:30,ke:[0,1,4,6,7,8,18,21,22,30],keep:0,kei:30,keita:30,keith:30,kela:30,kemri:30,kenji:30,kenneth:30,kenya:[0,1,4,8,10,12,18,23],kenyan:30,keppel:30,kept:30,kern:30,kernel:6,kerr:30,kevin:30,kh:26,kiaxi:30,kib:[6,7],kidima:30,kientega:17,kigozi:30,kihihi:30,kilama:30,kilamba:30,kilifi:30,kilimanjaro:30,kima:17,kimberli:30,kingdom:30,kinyoki:30,kisinza:30,kissidoug:30,kisumu:30,kit:30,kitau:30,kleang:[25,26,27],kleinschmidt:30,km:30,knockdown:30,know:[0,6,7,21,22,25,26],known:[0,8,21,23,30],koekemo:[0,6,7],koffi:15,koforidua:30,komaswa:30,kombila:30,konat:30,kone:30,koraboh:30,kou:30,koudou:30,koulikoro:30,koundara:30,kovana:30,kuklinski:30,kuma:30,kumbungu:6,kunda:30,kv:25,kwang:30,kwiatkowski:30,kyann:30,l3:30,l995f:30,l:[14,30],la:30,lab:[8,21,30],label:[21,23,29,30],laboratoir:30,laboratori:[27,30],lagdo:30,lai:30,laid:30,lake:30,lama:[4,10],lambda:30,land:30,landscap:30,lane:23,larg:[7,22,26,30,31],larger:23,largest:25,larva:30,larval:30,lassana:30,late:[25,26],later:30,latitud:[6,7,21,22,25,26,27],lauderdal:0,launch:[6,21,25],laurent:[25,26,27],lavoi:30,lawniczak:[0,1,12],lawrenc:30,layer:6,le:30,lead:23,leaf:23,learn:23,least:23,leav:23,led:[0,27],leffler:23,leg:30,legoff:30,lehmann:[9,11],leibala:30,len:[6,21,25],length:[22,25,30],less:[6,21,23,30],let:[6,21,25],letter:[6,8,21],level:30,libitum:30,librari:23,librevil:30,life:30,light:30,like:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30],likelihood:23,limit:[6,21,23,30],lindsai:30,line:[7,22,26,31],link:[7,22,26],linux:[7,22,26],lisboa:30,lisbon:30,list:[0,1,2,3,4,7,8,10,11,12,13,14,15,16,17,18,22,30],literatur:[1,2,10,16,17,18],live:30,liverpool:[23,30],lizett:6,ljmu:30,ll:[6,21,25],llin:[15,17],llineup:[15,17],lo_:22,load:[6,21,25],lobo:30,loc:[6,21],loc_cohort:25,loc_cohort_sampl:[6,21],loc_funestu:6,loc_gambia:21,loc_pass:[6,21,25],loc_seg:[6,21],local:[6,7,21,22,23,25,26,27,30],locat:[0,6,7,8,21,22,23,25,26,27,30,31],loci:[21,22,30],locu:30,log:31,login:31,logist:23,london:30,longipalpi:1,longitud:[6,7,21,22,25,26,27],longitudin:27,look:19,lookseq:30,loua:30,loughlin:30,love:[6,7,21,22,25,26],low:[6,7,21,22,23,25,30],lower:[23,30],loyc:30,lshtm:30,lstm:[9,21],lstmed:30,lt:[6,21,25],lua001:21,lua002:21,lua004:21,lua006:21,lua007:21,lua047:21,lua049:21,lua051:21,lua061:21,lua078:21,lua:21,lua_colu_2009:21,lua_colu_2009_04:21,lua_luanda_colu_2009:21,lua_luanda_colu_2009_04:21,luanda:[21,30],luc:30,luca:[23,30],lund:30,lutt:30,lydi:30,lynd:30,m:[7,21,22,30],mabogini:30,mac:30,macenta:30,machin:[23,31],maco:7,madagascar:[18,30],made:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,21,22,23,30],madina:30,magesa:30,mai:[0,6,7,8,21,22,23,25,26,30,31],maiga:30,mailto:31,main:30,mainland:30,mainli:30,maintain:30,mair:30,majet:30,majidah:30,major:[0,1,12,15,16,18,23,27,30],make:[0,6,21,23,25],makumira:30,malaria:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,19,27,30,31],malariagen:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,27,31],malariagen_data:[0,5,6,20,21,24,25,29],malatti:30,malawi:[0,1,8],male:[6,21,23,30],mali:[1,8,9,10,11,13,18],malian:[9,11],malima:30,mamad:30,manag:30,mancini:30,manda:30,mango:30,mani:[0,6,25],manifest:[6,7,21,22],mansk:30,manual:[23,30],manufactur:23,map:[0,8,22,23,26,30],mara:0,maranda:30,marc:30,march:30,marcia:30,marco:30,mari:30,maria:30,mark:[7,22,26,30],marker:22,markov:23,marsh:30,martin:[21,30],maryam:30,maryland:30,maryvonn:30,mask:[6,21,25],massiv:30,master:30,masu:30,match:[6,21,25],mater:30,materi:19,mathanga:30,mathurin:30,matia:30,matiya:30,matowo:30,maureen:30,mawejj:30,max_af:21,max_allel:[6,21,25],maximum:23,maxwel:30,mayo:30,mayott:8,mb:[21,22,25],mbogo:30,mbp:[7,22],mburu:30,mccann:30,md:[7,30],mead:30,meal:30,mean:[6,7,21,22,23,30],meant:23,med:30,median:[23,30],medic:30,medicin:[23,30],medicina:30,mehaffei:30,meillon:30,mela:[10,16,18,30],melissa:30,member:[8,23,30],memori:[6,21,25],mendelian:[23,30],mendez:30,menu:31,merg:[7,22,23],merged_vari:[7,22],meru:[10,18,30],mesa:30,mesamalaria:30,meso:30,meta:[6,7,21,22,25,26],metadata:[8,23,27],method:[6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,27,28,30,31],methyl:30,metric:23,mg:22,mib:6,michael:30,michel:30,micro:30,microb:30,microbiolog:30,microsatellit:30,microscop:30,midega:30,might:[7,22],migrat:[9,11],mile:[23,30],million:[6,21],milwauke:30,min:[7,22],miniatur:30,minim:23,minimis:31,minimu:[26,27,29],minimum:23,minimus1:25,minja:30,minneapoli:30,minut:[6,21],miss:[6,21,23,25],mit:23,mivegec:30,mix:30,mkdir:[7,22,26],ml:[8,9,11,21,22,27,30],mmp:30,mn:30,modal:[21,23],modar:30,mode:23,model:[6,7],modif:23,modifi:30,mok:[25,27],mol:30,molbev:30,molecular:30,monicah:30,monitor:[0,16,30,31],monomtenga:30,month:[6,7,21,22,25,26,30],montpelli:30,moor:30,mopti:30,more:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,27,30,31],moriboboug:30,morn:30,morpholog:30,mortal:30,mose:30,mosha:30,moshi:30,mosquito:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30,31],most:[21,22,23,30,31],mother:30,motinho:6,mount:30,mourou:30,moussa:30,mouth:30,mozambican:30,mozambiqu:[0,1,6,8],mozf_1314:6,mozf_1315:6,mozf_1317:6,mozf_1319:6,mozf_1323:6,mq:[7,22,23],mra:30,mrcg:30,mrtc:30,msangi:30,msx087:30,mtsanga:30,much:30,muheza:30,muleba:[1,15,30],multi:[0,1,6,7,10,13,14,16,17,18,21,22,25,26,30],multiallel:23,multipl:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,18,22,27,30],multiplex:23,multipli:23,multiprocess:7,multithread:7,munhenga:[15,18],municip:30,musa:30,muscarin:21,museum:30,muskavitch:30,must:21,mutat:[23,30],mve:30,mw:[1,8,21,22,30],mwangangi:30,mwesigwa:30,mweya:30,mybind:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21],myriad:30,mz:[0,6,7,8,21,22,30],mzilahowa:30,n:[6,7,21,22,23,25,26,30],n_pass:25,n_pass_seg:[6,21,25],n_site:25,na:30,nacion:30,nagongera:30,nakasero:30,name:[7,21],nan:[21,25],nanarrai:21,nankana:[1,12,16],nat:30,natacha:30,nation:[27,30],natur:[0,8,23,30],nbesansk:30,nbsp:[25,27],ncbi:30,ncomms1672:30,nd:30,ndarrai:[6,21,25],neafsei:[23,30],nearbi:30,nearest:23,nebul:23,necessarili:[6,21],need:[1,2,3,4,6,7,21,22,25,31],neg:23,neighbourhood:30,neil:30,nelson:30,net:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,30,31],netherland:30,network:[6,7,14,16,28,31],nextec:27,ng:[1,17,23],ngayo:30,ngwa:18,niaid:[9,27],niang:[4,10],niar:30,nich:30,nicola:30,niel:[4,10],nigeria:[0,1,17,18],night:30,nih:[9,27,30],nimr:30,niono:30,njabakunda:30,njau:30,nkolondom:30,nlm:30,no_cov:22,node:[6,21,23,25],nohal:30,nomenclatur:30,non:[6,7,21,22,23],none:[6,23],nonmajor:[7,22],noor:30,nora:30,norm:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23],normal:[6,21],normalis:23,north:30,northeast:30,northern:6,note:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,31],notebook:[6,7,21,22,25,26],notr:30,noufou:30,nov:[25,26],nova:30,novel:30,novemb:[9,11,12,13,14,15,16,17,30],novo:23,now:[6,21,25],np:[6,21,25],np_fune_2017:6,np_fune_2017_07:6,np_fune_2017_08:6,np_fune_2017_q3:6,np_kumbungu_fune_2017:6,np_kumbungu_fune_2017_07:6,np_kumbungu_fune_2017_08:6,np_kumbungu_fune_2017_q3:6,np_tolon_fune_2017:6,np_tolon_fune_2017_07:6,np_tolon_fune_2017_08:6,np_tolon_fune_2017_q3:6,nuclear:23,nucleotid:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30],number:[0,1,8,9,10,11,12,13,14,15,16,17,18,25,27,29,30],numer:30,numpi:[6,21,25],nwakanma:30,nyado:30,nyangweso:30,nzerekor:30,nzovu:30,o:[7,21,30],object:[0,6,7,8,21,22,23,25,26],objectdask:[6,21],objectnan:21,observ:[6,7,21,22,23,25],observatori:[0,6,7],obtain:[6,7,21,22,23,30,31],occur:[23,30],occurr:30,oceac:30,ochieng:30,ochomo:[0,6,7],octob:30,offspr:30,often:30,oh:30,oil:30,ok:22,okedi:30,okello:30,okfr:1,okumu:[0,1,2,3,6,7],okyereko:30,olotu:30,oloughlin:[1,13,30],omitola:[1,17],omol:[1,17],onc:23,one:[1,2,6,7,9,10,17,21,22,23,25,27,28,30],ones:[6,7],ongo:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],onli:[0,6,7,8,21,22,23,25,30,31],onto:23,open:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27,30],openli:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27],oper:[6,7,21,22,23,25],operation:19,opondo:[14,30],optic:30,optimis:[23,31],option:[7,22],order:[6,21,29],org:[7,27,30],organis:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,30,31],organophosph:30,origin:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23,30],original_sample_id:[25,26],os:30,other:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30,31],otherwis:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23,30],ouagadoug:30,ouassorola:30,oulena:30,oumou:30,our:[1,2,3,4,6,7,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,31],out:[0,6,8,21,23,25,27,30],outbreak:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],outdoor:30,output:[6,7,21,22,23],outsid:[0,23,30,31],ovari:30,over:[0,6,7,21,22,23,25,27,30],overgaard:30,overlap:[6,7,21,22,23],overnight:30,overview:[0,8],ow:30,own:[0,7,8,22,30],ox1:30,ox:30,oxford:30,oxfordmartin:30,p450:30,p:[6,21,25,30],p_fune_2015:6,p_fune_2015_08:6,p_fune_2015_q3:6,p_palma_fune_2015:6,p_palma_fune_2015_08:6,p_palma_fune_2015_q3:6,paaijman:[0,6,7],packag:[5,6,20,21,24,25,29],page:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,27,28,30],pain:30,pair:[6,21,23,30],pairwis:23,pala:[22,30],palm:30,palma:6,paludism:30,pamca:[1,2,14,15,16,18,19],pamgen:[10,14,16,18],pan:[14,16],panda:[6,21,25],panel:[6,21,23],paper:[0,27,30],paracentr:[23,30],parallel_process_count:7,paramet:[6,21,23],parasit:[1,12,16,18,30],parasitolog:[27,30],parassitologia:30,parensi:1,parent:[6,21,23,30],pari:30,park:30,parsimoni:30,part:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,22,27,30],parti:31,particular:[6,7,21,22,23,25,26,30],particularli:23,partit:30,partner_sample_id:[6,7,21,22,25,26],pascal:30,pasqual:30,pass:[6,21,22,23],pasteur:30,patch:29,path:[7,22,26],pathogen:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],patric:30,patricia:30,patrick:30,pattern:23,patton:30,paul:30,pc1:23,pc2:23,pca_cohort:[25,26],pcr:30,peak:30,pedigre:23,peopl:30,per:[7,22,23],per_sampl:[7,22],percentag:23,percentil:23,perenni:30,perform:[6,19,21,22,23,25,30,31],peri:30,perman:30,permethrin:30,permiss:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,31],permit:[0,1,2,3,4,9,10,11,12,13,14,15,16,17,18],peter:30,petrarca:30,pgen:30,phase:[1,6,7,21,22,28,30],phenol:30,phenoloxidas:21,phenotyp:14,philbert:30,philip:30,philippa:30,phiri:30,phylogenom:10,physic:[6,21,25],pie:30,pimperena:30,pinto:[21,30],pip:[0,6,21,25],pipelin:[7,22,23],pipini:30,pirimipho:30,pivot_t:25,place:[6,7,21,22,25,26,30],plan:[0,31],plantat:30,plasmodium:[0,1,17,18,30],plastic:30,plate:[27,30],platform:23,plausibl:23,pleas:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,24,25,26,27,28,29,31],plo:30,ploidi:[6,21,25],plot:[19,30],pmc2988034:30,pmc3543752:30,pmc3606099:30,pmc4124135:30,pmc:30,po:[6,21,25,30],point:23,polici:31,pollut:30,polymeras:30,polymorph:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30],polyten:30,pombi:30,pool:30,popul:[1,2,6,12,15,16,18,21,25,26,30],portug:30,posit:[6,7,21,22,23],possibl:[6,21,23,25,30],potenti:[23,30],poupardin:30,pour:30,power:[6,21],pradin:30,praso:30,pre:[1,2,3,4,6],preah:[25,26,27],precis:[8,23],predict:23,predomin:30,prefix:[7,22,26],preliminari:[22,30],prepar:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23,30],presenc:[0,1,6,17,18,21,23,30],present:[0,22,23,26,30],preserv:30,presum:23,previou:[23,30],previous:[23,30],primari:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30],primer:30,princip:[18,23],principl:0,print:[6,21,25],prior:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,30,31],probabl:[7,22,23],probe:30,problem:7,problemat:30,proceed:30,process:[23,30],produc:[6,7,23,30],product:23,progeni:[23,30],programa:30,programm:[1,2,14,15,16,18,30],progress:[6,21,25],progressbar:[6,21,25],project:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,28,30],prone:30,proport:[23,30],prot:21,protein:21,protocol:[23,30],protopopoff:30,provid:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,28,29,30,31],provinc:[27,30],provis:31,proxim:[6,7,21,22,30],pt:30,pubblica:30,publicli:[1,2,3,4,6,7,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26],publish:[0,30],pubm:30,puddl:30,pupa:30,pure:30,puregen:30,purpos:[8,27,31],pursat:27,put:[21,23],pv:[7,22,25,26],py:[21,25],pypi:25,pyrethroid:30,pyrethrum:30,pysam:23,python:[5,6,7,20,21,24,25,29],q10:22,q30:22,q7pkf8:21,q:[0,6,21,25,30],q_mean:22,q_std:22,qiagen:30,quadriallel:25,quadriannulatu:[10,18],qualiti:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,27],quarterli:27,queri:[6,21,25],question:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,21,27,31],r:[7,22,26,30],radiat:30,rain:30,raini:30,rais:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27,30],ramphul:30,ran:[22,26],random:23,randomis:30,randomli:[23,30],rang:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,27,30],ranson:30,rapid:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],rare:23,rasman:30,rasmussen:30,ratanakiri:27,rate:[23,30],rather:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23],ratio:23,rational:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],raw:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,27],raymond:30,rdna:30,re:30,reach:[30,31],reaction:30,read:[6,7,25,29,30],readi:[22,26,28],readm:7,realign:23,realignertargetcr:23,rear:30,reason:31,rebuild:10,receiv:23,recent:[6,21,30],receptor:21,recherch:30,recogn:30,recomput:23,record:[21,23,30],reddi:30,reduc:30,refer:[6,21,23],reflect:30,reg:21,regard:[6,7,21,22,23,25],regardless:[7,22],regier:30,reginald:30,region:[6,7,8,21,22,23,25,26,30,31],regna:30,reidenbach:30,rel:[22,23,30],relat:7,related:23,releas:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,26,27,30,31],relev:19,reliabl:[6,7,21,22,23,25,30],remain:[1,2,3,4,6,9,10,11,12,13,14,15,16,17,18,21,23,31],rememb:8,remov:[7,22,23,26,30],rep:30,replac:23,repo:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27],report:[19,22,23,30],repositori:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23],repres:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,23,25,30],republ:[0,1,8,14],request:22,requir:[6,7,21,22,23,25,26,30,31],rerun:29,research:[0,8,9,27,30],reset_index:[6,21],residu:30,resist:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,21,22,30],resolv:[6,21,22,23],resourc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,27,28,29,31],respond:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],respons:22,rest:30,restart:6,restrict:30,result:[6,7,19,21,23,27,30],retain:23,retriev:30,reveal:[10,27,30],review:30,rflp:30,ribosom:30,ric:30,rice:30,richard:30,ridl:30,riehl:30,rippon:30,risk:30,ritha:30,river:30,riversid:30,rk1:25,rk2:25,rn:[7,22],rna:30,rnalat:30,road:30,roadsid:30,robert:30,rodolph:30,rodrigu:30,roelant:30,rohatgi:30,roma:30,romain:30,rome:30,root:[7,22,23],rosario:30,row:[6,7,21,22,25,26],rowland:30,rsync:[7,22,26],rua:30,run:[7,22,23,25,26,30,31],runtim:31,rural:30,russia:30,ruth:30,s12879:30,s12936:30,s1:[6,21,25],s1dask:[6,21,25],s24:25,s24dask:25,s3:[7,22,26],s:[0,1,2,3,4,6,9,10,11,12,13,14,15,16,17,18,21,22,23,25,27,30],sabatini:30,sacriba:30,safim:30,sagnon:30,sahara:30,sahel:[9,11],salaam:30,sama:30,samantha:30,samba:30,same:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,23,25,30],sampl:29,sample_count:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22],sample_coverage_vari:[6,21],sample_id:[6,7,21,22,25,26],sample_is_high_vari:[6,21],sample_metadata:[6,21,25],sample_queri:21,sample_set:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22],samples_phas:[6,21],samson:30,samuel:[6,7,30],san:[25,27,30],sanger:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,18,22,23,26,27,30],sanger_sample_id:[25,26],sanita:30,sankar:30,santolamazza:30,sao:18,sapienza:30,sarah:30,sare:30,savanna:30,savannah:30,save:22,saya:[25,27],sc_20220908:[6,7],scale:30,scan:[6,21],scatter:30,school:[23,30],sci:30,scienc:[30,31],scientif:19,scientifiqu:30,scikit:[6,21,23,25],score:30,scott:30,screen:[0,1,17,18,30],sea:30,search:22,season:[1,15,25,26,30],second:[6,7,21,23,25,30],section:[21,22],see:[6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,25,26,27,29,30,31],segreg:[6,21,23],sekou:30,select:[6,18,21,22,23,25,30,31],semi:30,seneg:[4,10],seni:30,sent:22,separ:[0,6,7,21,22,23,27,30],septemb:30,seq:25,sequenc:[6,7,21,25,28,30],servic:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,27,31],set:[23,25],set_capt:25,set_index:[6,21],seven:30,sever:[0,1,2,3,4,7,8,9,10,11,12,13,14,15,16,17,18,22],sex_cal:[6,7,21,22],shandala:30,shape:[6,21,25],shapeit4:23,sharakhov:30,sharakhova:30,share:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,23],sharp:30,sheet:30,shelter:30,shik:30,should:23,show:26,shown:[6,21,25,30],shrubland:30,side:30,sidi:30,signal:[6,21],signific:23,significantli:30,silenc:[6,21],silica:[27,30],silwood:30,simard:30,similar:23,simon:30,simpl:[25,30],simpli:21,simultan:30,sinc:30,sindato:30,sinex:30,singl:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30],singleton:23,site:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,26,27,30],site_filt:[6,7,22],site_filters_analysi:6,site_mask:25,six:[23,30],size:[6,21,23],sj:30,skew:23,skip:31,sl5:30,slice:[6,21,25],slightli:23,slope:30,slotman:30,small:[1,2,23,25,30],smith:30,sn:[4,10],snounou:30,snow:30,snp:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27,29],snp_call:[6,21,25],snp_genotyp:[7,22],snp_genotypes_vcf:[7,22,26],snp_haplotyp:[7,22],so:[6,7,21,22,23,25,31],soc:30,softwar:[6,21],sogolomboug:30,solut:30,solv:30,some:[0,6,7,8,21,22,23,25],soon:31,sort:30,sourc:[21,23,30],souroukoudinga:30,sousa:30,south:[1,10,15,18,30],southeast:27,southern:30,sow:30,space:[22,23],spatiotempor:0,speci:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,25,27,30],special:[21,30],speciat:30,species_aim:22,species_calls_aim_20220528:22,species_gambcolu_arabiensi:22,species_gambiae_coluzzii:22,specif:[0,6,7,8,21,22,23],specifi:0,specimen:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,23,25,26,27,30],split_large_chunk:[6,21,25],sporozoit:30,sprai:30,spread:[1,14,23,30],squar:23,srep46451:30,ss:30,st:[25,26,27],staedk:30,staff:23,stalker:30,stand:[6,21],standard:[30,31],start:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,27,28],state:[1,2,3,4,6,7,9,10,11,12,13,14,15,16,17,18,21,22,25,26,30],station:30,statist:[6,7,19],statu:[23,30],steen:30,step:[7,23],stephan:30,stephani:30,stephen:30,steve:30,steven:30,still:7,stlaurent:26,stochast:23,storag:[6,7,21,22,25,26,27,31],store:[6,7,21,22,25,26,27,30,31],strategi:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30],street:30,strengthen:15,string:[6,21],strongli:30,structur:[0,7,15,18,22,25,26,30],studi:[6,7,21,22,25,28],study_id:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18],study_url:[6,7],style:25,subcounti:30,subdivid:22,subgroup:30,subject:[0,6,8,21,23,30,31],submit:[0,23,31],subsampled_cohort:[25,26],subsect:[7,22,23],subsequ:30,subset:[7,22,23,25],substanti:[22,31],suburb:30,suburban:30,success:23,successfulli:23,sudan:30,sudanian:30,suffici:[7,22],suffix:8,sugar:30,suggest:30,suiss:30,suitabl:[21,22,23,25],sum:25,summari:[6,7,21,25],summaris:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,21],suna:30,sunset:30,supplement:30,support:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,23,31],sur:30,surround:30,survei:30,surveil:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,27,31],suscept:30,suspend:31,swampland:30,swarm:30,sy:30,sympatri:30,synchron:[7,22],system:[7,22,26,30],systemat:30,t:[6,7,21,22,23,25,30],tab:[7,22],tabix:[7,22],tabl:19,tag:23,takan:30,take:[6,7,21,22,23],taken:30,takken:30,takoradi:30,talisuna:30,tankonjala:30,tankular:30,tanzania:[0,1,2,3,8,10,16,18,23],tanzanian:30,tarbiat:30,target:[1,13,23,30],targetmalaria:30,tarim:30,task:[21,25],taxa:30,taxon:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21],tb:21,tbi:[7,22],td:25,team:23,tech:30,technician:30,technolog:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27],tehran:30,templat:30,temporari:30,temporarili:31,tennessen:17,terlouw:30,term:[6,21],termin:[7,22,23,26],terra:[23,31],test:30,tetramin:30,text:[7,22],tg:11,than:[1,2,3,4,6,9,10,11,12,13,14,15,16,17,18,21,23,30],thank:[23,30],thei:[0,7,22,30,31],them:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18],themba:30,themselv:6,therefor:[25,30],thes:[7,22],thesi:30,thi:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,28,30,31],thicket:30,thierri:30,third:[6,8,21,25,30,31],thmar:[25,27],thoma:30,those:23,threat:[1,2,3,4,9,10,11,12,13,14,15,16,17,18],three:[6,7,8,21,22,25,27,30],threshold:23,thrive:30,through:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27,30],throughout:[6,7,21,22,23,25,26,30],thu:[6,21,23],thymin:[6,21],tiassal:30,tibati:30,tienegueboug:30,time:[0,6,7,21,22,25,26],times2784:21,times36:6,times656:6,times82:21,tissu:30,tjmidega:30,to_haplotyp:[6,21],togeth:[21,22,23],togo:11,tolon:6,toma:30,tome:18,tomsk:30,took:[23,30],tool:[7,22,26],top:[6,21,23,25],topographi:30,tororo:30,torr:30,total:[8,23,25],touch:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26],toumani:30,tour:30,town:30,townson:30,track:30,trai:30,train:[19,23,30],tran:30,transect:30,transfer:[6,21,25,31],transit:[23,30],transmiss:30,transmit:30,transport:30,traor:30,trap:30,tree:[6,7,23,30],trembl:21,trial:[18,30],triallel:25,trim:[7,22],troco:30,trop:30,tropic:[23,30],trstmh:30,truli:23,trust:30,tsv:[7,22],tube:[27,30],tumaini:30,tungu:30,turn:30,twenti:30,twice:23,twifo:30,two:[6,7,8,18,21,23,27,30],type:[1,2,3,4,6,7,9,10,11,12,13,14,15,16,17,18,21,22,25,30],tz:[0,1,2,3,6,7,8,16,21,22,30],u24:21,u24dask:21,u36:6,u36dask:6,ug:[1,8,12,15,17,21,22,30],uganda:[0,1,8,12,15,17,18],uint8:[6,21,25],uint8dask:[6,21,25],uk:[0,7,9,22,26,30],umberto:30,umr:30,unassign:[8,9,10,11,12,13,14,15,16,17,18],unbalanc:23,uncertain:23,under:[6,23,30],understand:[0,14],undertaken:[23,30],unexpect:31,unifiedgenotyp:23,union:18,uniprotkb:21,uniqu:[21,23,25],uniroma1:30,unit:[6,7,21,22,25,26,30],univ:30,univers:30,universidad:30,unl:30,unless:[1,2,3,4,9,10,11,12,13,14,15,16,17,18,30],unreli:23,unstabl:30,until:30,unusu:30,up:[6,7,21,22,23,25],updat:6,upgrad:31,upland:30,upload:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18],upon:[0,30],urban:30,url:[6,7,21,22,26,30],urvashi:30,us:[7,19,22,25,26,29,30],usa:[9,27,30],user:[7,31],usual:[22,23,30],v1:[7,26],v3:22,v:[23,30],vaccin:30,valencia:30,valid:23,valu:[6,21,23,25,26,30],valuabl:[0,8,27],vamsi:30,van:30,vaneedeni:1,vari:30,variabl:[6,21,25],varianc:[6,7,21,22,23],variant:[6,7,21,22,25,28,29],variant_allel:[6,21,25],variant_ciend:[6,21],variant_cipo:[6,21],variant_contig:[6,21,25],variant_end:[6,21],variant_endbreakpointmethod:21,variant_filter_pass:[6,21,25],variant_filter_pass_:[6,21],variant_filter_pass_arab:21,variant_filter_pass_funestu:6,variant_filter_pass_gamb_colu:21,variant_filter_pass_gamb_colu_arab:21,variant_id:[6,21],variant_posit:[6,21,25],variant_region:21,variant_startbreakpointmethod:21,variat:[8,23,30],variou:[6,21,25],vast:23,vb:21,vbs09378:[25,26],vbs09382:[25,26],vbs09397:[25,26],vbs09460:[25,26],vbs09466:[25,26],vbs09467:26,vbs09477:26,vbs09482:26,vbs09483:26,vbs16624:25,vbs16625:25,vbs16626:25,vbs16628:25,vbs16630:25,vbs24195:[6,7],vbs24195_cnv_hmm:7,vbs24196:[6,7],vbs24197:[6,7],vbs24198:[6,7],vbs24199:[6,7],vbs24200:7,vbs24201:[6,7],vbs24202:7,vbs24203:7,vbs24213:6,vbs24216:6,vbs24534:6,vbs24535:6,vbs24536:6,vbs24537:6,vbs24539:6,vcf:23,ve:[6,21,25],vector:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,25,26,27,30],veget:30,veri:[21,30],verif:31,verili:30,vernick:30,version:[6,21,23,29,30],versu:22,vertex:31,vet:30,veterinari:30,vgsc:30,via:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,30,31],vial:30,viana:30,vicent:30,victoria:30,vid:21,video:31,view:[7,22,23,31],viewer:30,vihear:27,villag:[22,30],vincent:30,vincenzo:30,virginia:30,virtual:31,visit:[0,1,2,3,4,5,8,9,10,11,12,13,14,15,16,17,18,20,22,24,27,28,30],vm:31,vmf00004:9,vmf00013:[1,12],vmf00014:12,vmf00015:11,vmf00025:[1,12],vmf00028:12,vmf00029:12,vmf00043:[0,6,7],vmf00044:[0,6,7],vmf00045:[0,6,7],vmf00046:12,vmf00047:[1,12],vmf00050:11,vmf00051:11,vmf00052:11,vmf00054:11,vmf00067:[1,11],vmf00088:16,vmf00090:[0,6,7],vmf00094:[0,6,7],vmf00095:[0,6,7],vmf00095_funestus_2rl_phas:7,vmf00095_funestus_cnv_coverage_cal:7,vmf00099:[0,6,7],vmf00101:[0,6,7],vmf00102:16,vmf00106:[1,13],vmf00140:13,vmf00149:[1,13],vmf00160:14,vmf00161:14,vmf00162:14,vmf00164:[1,14],vmf00165:15,vmf00168:15,vmf00173:15,vmf00176:[1,15],vmf00178:15,vmf00185:16,vmf00193:16,vmf00197:16,vmf00202:16,vmf00208:16,vmf00212:16,vmf00218:18,vmf00219:[1,17],vmf00222:18,vmf00227:[2,18],vmf00228:18,vmf00232:18,vmf00235:18,vmf00242:18,vmf00244:10,vmf00246:18,vmf00248:1,vmf00250:[4,10],vmf00252:2,vmf00259:[4,10],vmf00261:3,vmf00281:4,vo:[0,1,2,3,4,6,7,9,10,11,12,13,14,15,16,17,18,26],vo_afun_releas:[6,7],vo_afun_release_master_us_central1:6,vo_agam_output:22,vo_agam_releas:[21,22],vo_amin_releas:[25,26],vt:30,vugt:30,w:30,wa:[6,7,21,22,23,25,26,27,30],wageningen:30,wai:[6,21,23,25],waiv:[11,12],wali:30,walkthrough:31,wambua:30,want:[0,6,7,8,21,22,25,26],warn:[6,21],water:30,watsenga:[1,14],watsengan:1,wc1e:30,wdl:23,we:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30,31],web:22,webpag:[0,1,2,3,4,10,11,12,13,14,15,16,17,18],websit:[1,2,3,4,6,9,10,11,12,13,14,15,16,17,18,21,22,31],weetman:30,welcom:28,well:[23,30],wellcom:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27,30],were:[1,6,7,8,21,22,23,25,26,27,29,30],west:[0,1,17,23,30],western:30,wet:[25,26],wga:23,wget:[7,22,26],wgs_snp_data:[7,22,26],whatshap:23,whatsoev:23,wheel:[21,25],when:[1,2,3,4,6,7,21,22,23,25,26,30,31],where:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,29,30],whether:[7,21,22],which:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,25,26,27,30,31],white:30,who:[0,8,30],wi:30,wide:[6,7,21,22,29],widespread:27,wild:[8,21,22,23,30],wildlif:30,wilkerson:30,wilkin:30,willem:30,william:30,wim:30,wind:30,window:[6,7,21,22,23,30],winifrida:30,wisconsin:30,within:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30,31],without:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,27,30],wo:6,won:[7,22],wondji:[0,6,7],woodland:30,work:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,27,31],workbench:31,workspac:31,would:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30],wrap:[6,21],wrapper:[6,21,25],wright:30,www:[6,7,22,30,31],x27:[6,21,25],x:[6,7,8,21,22,23,30],xag:23,xarrai:[6,21,25],xavier:30,y:30,yahoo:30,yallal:30,yanfolila:30,yao:30,yawson:[1,11,13,30],year:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,30],yeka:30,yey:30,yield:[23,30],yopougon:30,you:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,29],youden:23,your:[0,6,7,8,21,22,26,31],yourself:[6,21,25],z:[7,22,30],za:[15,18],zambia:[0,1,15,18],zemb:30,zeneti:30,zero:23,zimbabw:10,zip:[7,22],zm:[1,15],zone:30,zoogeograph:30,zoologi:30,zootaxa:30,zymo:30},titles:["Af1.0  (<em>Anopheles funestus</em> Project Phase 1 Data Release)","Af1.1","Af1.2","Af1.3","Af1.4","Af1 API","Af1 cloud data access","Af1 data downloads","Ag3.0 (Ag1000G phase 3)","Ag3.1","Ag3.10","Ag3.2","Ag3.3","Ag3.4","Ag3.5","Ag3.6","Ag3.7","Ag3.8","Ag3.9","Ag3 analysis","Ag3 API","Ag3 cloud data access","Ag3 data downloads","Ag3 sequencing and variant calling methods","Amin1 API","Amin1.0 cloud data access","Amin1.0 data downloads","Amin1.0","MalariaGEN vector data user guide","Release notes","Ag1000G partner studies","Vector Observatory Data Access"],titleterms:{"0":[0,8,25,26,27],"02":29,"03":29,"04":29,"07":29,"09":29,"1":[0,1,9,30,31],"10":10,"11":29,"12":29,"14":29,"15":29,"2":[2,11,30,31],"2021":29,"2022":29,"3":[3,8,12,30,31],"4":[4,13,31],"5":14,"6":15,"7":16,"8":17,"9":18,"c\u00f4te":30,"public":30,The:30,access:[6,21,25,31],account:31,acknowledg:[23,30],af1:[0,1,2,3,4,5,6,7],african:30,ag1000g:[8,30],ag3:[8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23],aim:23,align:[22,23,26],all:23,allel:[6,7,21,22,23,25],amin1:[24,25,26,27],an:23,analys:23,analysi:19,ancestri:23,angola:30,anomali:23,anophel:[0,28],api:[5,20,24],appendic:23,ar:31,arabiensi:23,assign:23,authent:31,bam:[22,26],bioko:30,bissau:30,burkina:30,calcul:23,call:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27],cameroon:30,central:30,citat:27,cloud:[6,21,25,31],cnv:[6,7,21,22,23],collect:[7,22],coloni:[23,30],coluzzii:23,commun:28,complex:28,comput:[6,21,25],congo:30,contamin:23,contributor:30,copi:[6,7,21,22,23],count:25,coverag:[6,7,21,22,23],credenti:31,cross:[23,30],d:30,data:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27,28,31],democrat:30,detect:23,discord:[21,22,23],discoveri:23,download:[7,22,26],ensur:31,exampl:[6,21,25],fair:31,faso:30,fastq:22,feedback:[6,7,21,22,25,26],fill:31,filter:[6,7,21,22,23,25],form:31,format:[7,22,26],funestu:[0,28],further:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27],gabon:30,gambia:[23,28,30],genom:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,25,27,28],genotyp:[6,7,21,22,25],ghana:30,googl:31,guid:28,guinea:30,haplotyp:[6,7,21,22,23],have:31,hmm:[6,7,21,22,23],host:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,25,26,27],identifi:23,infer:23,inform:[23,30],input:23,insecticid:23,island:30,ivoir:30,joint:23,kenya:30,larger:[6,21],latest:31,loci:23,make:31,malaria:28,malariagen:28,malariagen_data:31,malawi:30,mali:30,marker:23,mayott:30,metadata:[6,7,21,22,25,26],method:23,minimu:28,model:23,mozambiqu:30,normal:23,note:[28,29],number:[6,7,21,22,23],observatori:[28,31],out:31,outlier:23,packag:31,panel:[7,22],partner:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27,28,30],pass:25,pca:23,phase:[0,8,23],popul:[0,8,23,27],posit:25,project:0,python:31,qc:23,raw:22,read:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,21,22,23,26,27],refer:[7,22,25,30],releas:[0,28,29],replic:23,republ:30,request:31,resist:23,resourc:30,run:[6,21],sampl:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,23,25,26,27,30],segreg:25,sequenc:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,22,23,26,27],set:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,21,22,30,31],setup:[6,21,25],sex:23,site:[6,7,21,22,23,25],snp:[6,7,21,22,23,25,26],speci:[22,23],specimen:[7,22],state:23,statist:23,step:31,studi:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27,30],subset:[6,21],suggest:[6,7,21,22,25,26],summari:23,sure:31,tanzania:30,technic:23,term:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,27,31],three:23,uganda:30,up:31,us:[0,1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,18,21,23,27,31],usag:31,user:28,variant:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27],variat:[6,7,21,22],vcf:[7,22,26],vector:[28,31],version:31,via:23,whole:[0,1,2,3,4,8,9,10,11,12,13,14,15,16,17,18,23,27],wide:23,you:31,zarr:[7,22]}})
\ No newline at end of file