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 |