From 7ceca6c59ee9b22f73e5b0a91cf6263c5a5d1e4e Mon Sep 17 00:00:00 2001
From: ahernank <ahernank@users.noreply.github.com>
Date: Mon, 19 Aug 2024 13:38:15 +0000
Subject: [PATCH] deploy: fd62c88f3ed4b4c967066e14ce6b5fe5921f7983

---
 _sources/af1/af1.4.ipynb |  715 +++++++++++++++++++++++
 af1/af1.4.html           | 1196 ++++++++++++++++++++++++++++++++++++++
 objects.inv              |  Bin 672 -> 681 bytes
 searchindex.js           |    2 +-
 4 files changed, 1912 insertions(+), 1 deletion(-)
 create mode 100644 _sources/af1/af1.4.ipynb
 create mode 100644 af1/af1.4.html

diff --git a/_sources/af1/af1.4.ipynb b/_sources/af1/af1.4.ipynb
new file mode 100644
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--- /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">
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+                    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>
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+ <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">
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+  <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">
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+        <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>
+
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+    <div class="article row">
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+                <h1>Af1.4</h1>
+                <!-- Table of contents -->
+                <div id="print-main-content">
+                    <div id="jb-print-toc">
+                        
+                        <div>
+                            <h2> Contents </h2>
+                        </div>
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+                            <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>
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+   * 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
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diff --git a/searchindex.js b/searchindex.js
index 630bec7..fe94bcc 100644
--- a/searchindex.js
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