fileId String | File ID. |
sampleId String | Sample ID. |
rawTotalSequences int | Total number of raw sequences. |
filteredSequences int | Number of filtered sequences. |
sequences int | Number of sequences. |
isSorted int | If 1 then file is sorted. |
firstFragments int | Number of 1st fragments. |
lastFragments int | Number of last fragments. |
readsMapped int | Number of reads mapped. |
readsMappedAndPaired int | Number of reads mapped and paired (paired-end technology bit set + both mates mapped). |
readsUnmapped int | Number of reads unmapped. |
readsProperlyPaired int | Number of reads properly paired (proper-pair bit set). |
readsPaired int | Number of reads paired (paired-end technology bit set). |
readsDuplicated int | Number of reads duplicated (PCR or optical duplicate bit set). |
readsMq0 int | Number of reads mapped and MQ=0. |
readsQcFailed int | Number of reads whose QC failed. |
nonPrimaryAlignments int | Number of non-primary alignments. |
totalLength int | Total length (ignores clipping). |
basesMapped int | Number of bases mapped (ignores clipping) |
basesMappedCigar int | Number of bases mapped taking into account the CIGAR codes (more accurate). |
basesTrimmed int | Number of bases trimmed. |
basesDuplicated int | Number of bases duplicated. |
mismatches int | Number of mismatches (from NM fields). |
errorRate Double | Error rate, i.e.: mismatches / bases mapped (cigar) |
averageLength Double | Average read length. |
maximumLength int | Maximum read length. |
averageQuality Double | Average quality. |
insertSizeAverage Double | Insert size average. |
insertSizeStandardDeviation Double | Standard deviation of the insert size. |
inwardOrientedPairs int | Number of inward oriented pairs. |
outwardOrientedPairs int | Number of outward oriented pairs. |
pairsWithOtherOrientation int | Number of pairs with other orientation. |
pairsOnDifferentChromosomes int | Number of pairs on different chromosomes. |
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