Skip to main content

Table 1 ngs_backbone filters for SNV selection.

From: ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

  Description and pass conditions Value
MAF Frequency of most frequent allele in the selected pool allele is less than 0.80
HVR Percentage of divergence in the unigene is smaller than or equal to 4
UCR No duplicated or fragment regions are detected by Blast --
I30 The distance from intron/exon boundary is greater than 30
CL The distance to ends of unigene is greater than 30
CS The distance from neighboring SNPs is greater than 60
CEF The SNV can be detected by endonuclease restriction --
VK Select the kind of marker: SNP or indel --
GF Frequency of most frequent allele in the selected libraries is less than 0.67