Table 2

Putative single nucleotide polymorphisms at different quality criteria
Filter SNP Transitions Transversions Ratio
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

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