FIELD	COUNT	DESC
Stranded_Rule_Code	0	Code for the strandedness rule used. 0 if data is unstranded, 1 if data is fr_firstStrand, 2 if data is fr_secondStrand.
READ_PAIR_OK	10849084	Number of reads or read-pairs that pass initial filters and are processed by QoRTs.
TOTAL_READ_PAIRS	10849084	Total number of reads or read-pairs found in the input file.
DROPPED_NOT_PROPER_PAIR	-1	Number of reads or read-pairs dropped because the 'not proper pair' SAM flag is raised.
DROPPED_READ_FAILS_VENDOR_QC	0	Number of reads or read-pairs that have the 'failed vendor QC' SAM flag raised.
DROPPED_MARKED_NOT_VALID	0	Number of reads or read-pairs dropped because marked 'not valid'
DROPPED_CHROMS_MISMATCH	-1	Number of read-pairs dropped because the paired reads align to different chromosomes
DROPPED_PAIR_STRANDS_MISMATCH	-1	Number of read-pairs dropped because the paired reads align to inconsistent strands
DROPPED_IGNORED_CHROMOSOME	0	Number of reads or read-pairs dropped because they align to chromosomes marked for ignoring
DROPPED_NOT_UNIQUE_ALIGNMENT	0	Number of reads or read-pairs dropped because they are not uniquely aligned to single genomic locus
DROPPED_NO_ALN_BLOCKS	0	Number of reads or read-pairs dropped because they do not have any alignment blocks (despite being marked as aligned)
DROPPED_NOT_MARKED_RG	-1	Number of reads or read-pairs dropped because they are not in the correct read group (or -1 if read-group filtering is not on)
KEPT_NOT_UNIQUE_ALIGNMENT	0	Number of reads or read-pairs kept despite not being uniquely aligned.
minObservedReadLength	51	The base-pair length of the smallest read
maxObservedReadLength	51	The base-pair length of the largest read
maxLegalPhredScore	41	The largest observed PHRED score.
IS_SINGLE_END	1	0 if data is paired-ended, 1 if data is single-ended
PREALIGNMENT_READ_CT	7014609	The number of reads found pre-alignment. Can be set using --seqReadCt or --rawfastq. -1 if unknown.
BENCHMARK_MinutesOnSamIteration	4.88	The number of minutes spent on the SAM iteration step.
BENCHMARK_MinutesPerMillionReads	0.45	The number of minutes per million reads spent on the SAM iteration step
BENCHMARK_MinutesPerMillionGoodReads	0.45	The number of minutes per million reads that passed the initial filtering step.
ReadPairs_AmbigGene	587145	Number of reads or read-pairs that map to a genomic area that includes regions covered by more than one gene.
ReadPairs_UniqueGene	9514970	Number of reads or read-pairs that map to a genomic area covered by exactly one gene
ReadPairs_UniqueGene_CDS	9494856	Number of reads or read-pairs that map to a genomic area covered by exactly one gene, and intersect at least partially with the coding region of that gene.
ReadPairs_UniqueGene_UTR	20114	Number of reads or read-pairs that map to a genomic area covered by exactly one gene, but that only cover the UTR (non-coding) regions.
ReadPairs_NoGene	746969	Number of reads or read-pairs that are not assigned to any gene.
ReadPairs_NoGene_Intron	9842	Number of reads or read-pairs that are not assigned to any gene, and that occur within an intronic region of one or more genes.
ReadPairs_NoGene_OneKbFromGene	723167	Number of reads or read-pairs that are not assigned to any gene, and that are within 1kb from one or more genes.
ReadPairs_NoGene_TenKbFromGene	13960	Number of reads or read-pairs that are not assigned to any gene, and that are within 10kb from one or more genes.
ReadPairs_NoGene_MiddleOfNowhere	0	Number of reads or read-pairs that are not assigned to any gene, and that are more than 10kb from the nearest gene
Genes_Total	6692	Number of known genes
Genes_WithZeroCounts	372	Number of genes with zero observed reads
Genes_WithNonzeroCounts	6320	Number of genes with 1 or more observed reads
AVG_GC	0.42254701779452103	Average GC fraction across all reads
AggregateGenes	5993	Number of aggregate genes
AggregateGenes_NoReads	121	Number of aggregate genes with 0 observed reads
AggregateGenes_WithReads	5872	Number of aggregate genes with 1 or more observed reads
SpliceLoci	2120	Number of splice loci observed
SpliceLoci_Known	342	Number of known splice loci
SpliceLoci_Known_NoReads	94	Number of known splice loci with 0 observed reads
SpliceLoci_Known_FewReads	17	Number of known splice loci with 1-3 observed reads
SpliceLoci_Known_ManyReads	231	Number of known splice loci with 4+ observed reads
SpliceLoci_Novel	1778	Number of novel splice loci observed
SpliceLoci_Novel_FewReads	1728	Number of novel splice loci observed with 1-3 observed reads
SpliceLoci_Novel_ManyReads	50	Number of novel splice loci observed with 4+ observed reads
SpliceEvents	90085	Number of observed splicing events (each read or read-pair that maps across a splice junction is a splice 'event')
SpliceEvents_KnownLoci	81824	Number of splice events covering known SJ loci
SpliceEvents_KnownLociWithFewReads	29	Number of splice events covering low-coverage known SJ loci
SpliceEvents_KnownLociWithManyReads	81795	Number of splice events covering high-coverage known SJ loci
SpliceEvents_NovelLoci	8261	Number of splice events covering noverl SJ loci
SpliceEvents_NovelLociWithFewReads	1833	Number of splice events covering low-coverage novel SJ loci
SpliceEvents_NovelLociWithManyReads	6428	Number of splice events covering high-coverage novel SJ loci
StrandTest_frFirstStrand	4594162	Number of reads or read-pairs that match the fr_FirstStrand strandedness rule
StrandTest_frSecondStrand	4982864	Number of reads or read-pairs that match the fr_secondstrand strandedness rule
StrandTest_ambig_genesFountOnBothStrands	525089	Number of reads or read-pairs where the strandedness is ambiguous due to there being genes on both strands
StrandTest_ambig_noGenes	746969	Number of reads or read-pairs where the strandedness is ambiguous due to there being no known genes.
StrandTest_ambig_other	0	Numebr of reads or read-pairs where the strandedness is ambiguous due to other reasons
StrandTest_STRANDEDNESS_MATCHES_INFERRED	1	1 if the strandedness appears to match the strandedness mode, 0 otherwise.
NumberOfChromosomesCovered	17	Number of chromosomes with 1 or more aligned reads.
deletionLoci	11058	Number of observed deletion loci
insertionLoci	4948	Number of observed insertion loci
deletionEventCt	12762	Number of times deletions are observed in a read
insertionEventCt	9084	Number of times insertions are observed in a read
highCoverageDeletionLoci	33	Number of high-coverage deletion loci.
highCoverageInsertionLoci	181	Number of high-coverage insertion loci
NumReadsAtMaxReadLength_R1	10849084	Number of read-1 reads at the max length.
NumReadsAtMaxReadLength_R2	0	Number of read-2 reads at the max length.
NumReadsTruncated_R1	0	Number of read-1 reads that are not at the max length.
NumReadsTruncated_R2	0	Number of read-2 reads that are not at the max length.
NumReadsTruncated_25pct_R1	0	Number of read-1 reads that are truncated to less than 25% of the max length
NumReadsTruncated_25pct_R2	0	Number of read-2 reads that are truncated to less than 25% of the max length
NumReadsTruncated_50pct_R1	0	Number of read-1 reads that are truncated to less than 50% of the max length
NumReadsTruncated_50pct_R2	0	Number of read-2 reads that are truncated to less than 50% of the max length
NumReadsTruncated_75pct_R1	0	Number of read-1 reads that are truncated to less than 75% of the max length
NumReadsTruncated_75pct_R2	0	Number of read-2 reads that are truncated to less than 75% of the max length
READ_LENGTH	51	The read length.
COMPLETED_WITHOUT_WARNING	0	0 if complete without throwing any warnings. 1 if warnings were thrown.
QoRTs_initTimeStamp	1535641810727	Time stamp for when QoRTs QC began.
QoRTs_samDoneTimeStamp	1535642109000	Time stamp for when QoRTs QC finished SAM iteration.
QoRTs_majorVer	1	QoRTs major version number
QoRTs_minorVer	3	QoRTs minor version number
QoRTs_patchVer	0	QoRTs patch version number
QoRTs_compileTimeStamp	1508514997	The timestamp for when the version of QoRTs was built.
COMPLETED_WITHOUT_ERROR	1	1 if QoRTs completed without errors. If QoRTs encountered an error, this file should not exist.