|Putative single nucleotide polymorphisms at different quality criteria|
|Sanger Qual > = 60||20,781||11,389||9,392||1.21|
|Sanger Qual > = 60 and AF [0.25, 0.75]||14,745||8,372||6,372||1.31|
|Sanger Qual > = 60 and AF [0.25, 0.75]||9,394||5,622||3,770||1.49|
|and Depth > = 20, DP4> = 10|
The effect of using different quality criteria for identifying SNPs. Sanger Qual = Sanger sequence quality, AF = Allele frequency, Depth = sequence depth at the base DP4 = Depth of the two variants according to the read direction. For details see the samtools specifications.
Chen et al.
Chen et al. BMC Genomics 2012 13:589 doi:10.1186/1471-2164-13-589