FYI, the public hiseq X10 data from BaseSpase use these 7 quality values. Heng
On Oct 9, 2014, at 11:46 AM, Tim Fennell <tfenn...@broadinstitute.org> wrote: > 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 ------------------------------------------------------------------------------ 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
