Recent versions of the Illumina instrument software have been configured to produce more broadly binned quality scores. The most likely explanation is that the 18 samples with only 7 distinct quality values are either newer or were produced on instruments that are configured this way. If so, it does not imply any problem with the data. Perhaps you can check with your sequencing core/vendor?
-t On Oct 9, 2014, at 10:59 AM, William Gilks <w.gi...@sussex.ac.uk> wrote: > Hi, > > I¹ve sequenced 200 fly genomes and generated qc data on the resultant bams > with Picard 1.77. > > In the multiplemetrics.quality_distribution_metrics output most samples > have a frequency value for every quality value from 5-41 (37 observations). > > However, 18 samples only have 7 observations, at quality values of > 6,15,22,27,33,37 and 40. > > Attached is a simple graph of all 200 samples, read mapping quality vs > frequency per sample. > > I¹m wondering if this is a problem with my input data or what. > > Any advice most welcome, > > William Gilks > ________________________________________ > > Research Fellow > School of Life Sciences > University of Sussex, United Kingdom > Tel +44(0)1273 678 559 > FAX +44(0)1273 877586 > URL http://www.sussex.ac.uk/lifesci/morrowlab/people > <http://www.sussex.ac.uk/lifesci/ebe/people/list/person/299309> > > > <qualDistr_200genomes_illuminaPE.png>------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk_______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
