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Table 2 Putative single nucleotide polymorphisms at different quality criteria

From: Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms

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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

    
  1. 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.
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BMC Genomics

ISSN: 1471-2164

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