Alignment Statistics



Sample Total reads Average read length (bp) Total yield (bp) Target regions (bp) Average throughput depth of target regions (X) Initial mappable reads Initial mappable reads (%) Non-redundant reads Non-redundant reads (%) On-target reads On-target reads (%) On-target Yield (bp) Mean depth of target regions (X)
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  •   · Total reads : Total Number of Reads.
  •   · Average read length(bp) : Average length of reads after trimming.
  •   · Total yield(bp) : Total number of bases sequenced.
  •   · Target regions(bp) : Target region size.
  •   · Average throughput depth of target regions(X) : {Total yield} / {Target regions}.
  •   · Initial mappable reads : Number of reads mapped to reference.
  •   · Initial mappable reads(%) : 100 * { Initial mappable reads} / {Total reads}.
  •   · Non-redundant reads : Number of de-duplicate reads from Picard tools.
  •   · Non-redundant reads(%) : 100 * {Non-redundant reads } / { Initial mappable reads}.
  •   · On-target reads : Number of reads mapped to target regions.
  •   · On-target reads(%) : 100 * {On-target reads} / {Non-redundant reads}.
  •   · On-target Yield(bp) : The sum of the bases in the final alignment to the target regions.
  •   · Mean depth of target regions(X) : {On-target yield} / {Target regions}.


Sample Number of on-target genotypes (>=1X) % Coverage of target regions (>=1X) Number of on-target genotypes (>=10X) % Coverage of target regions (>=10X) Number of on-target genotypes (>=20X) % Coverage of target regions (>=20X) Number of on-target genotypes (>=30X) % Coverage of target regions (>=30X) Number of on-target genotypes (>=50X) % Coverage of target regions (>=50X)
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  •   · % Coverage : The percentage of bases in target regions with a depth of coverage or greater.





Sample Fragment length median Standard deviation