Q2 is a legacy value; it's effectively Illumina's garbage value; they tend
to be bad bases even after recalibration. Q2 is what the machine produces
when it's read through a nucleotide repeat and has no real idea what the
bases are. See below: all the faint bases are Q2.
[image: Inline image 1]


On Mon, Jan 27, 2014 at 1:54 PM, Matt Massie <notifications@github.com>wrote:

> In
> adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/rdd/recalibration/ReadCovariates.scala:
>
> > @@ -28,27 +28,35 @@ object ReadCovariates {
> >  }
> >
> >  class ReadCovariates(val read: RichADAMRecord, qualByRG: QualByRG, covars: List[StandardCovariate],
> > -                     val dbSNP: SnpTable) extends Iterator[BaseCovariates] with Serializable {
> > +                     val dbSNP: SnpTable, val minQuality:Int = 2) extends Iterator[BaseCovariates] with Serializable {
>
> I think Phred 2 is P=0.63
>
>
> https://www.google.com/search?q=10+%5E+(-2%2F10)&oq=10+%5E+(-2%2F10)&aqs=chrome..69i57j0j69i64l2.7131j0j7&sourceid=chrome&espv=210&es_sm=119&ie=UTF-8
> )
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/bigdatagenomics/adam/pull/60/files#r9200596>
> .
>