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Table 2 SNP filtering criteria for SNP discovery

From: Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries

Criteria used for SNP calling Cut-off values
Minimum mapped read depth to the reference ≥ 3
Maximum mapped read depth to the reference X ¯ + 2sa
Consensus base ratio ≥ 0.9
Mapping quality score in SAMtools ≥ 20
Removal of homopolymer SNPs with base string length ≥ 3 bp
Removal of very close SNPs with gap between contiguous SNPs < 2 bp
  1. a X ¯ + 2s is the average read depth and standard deviation estimated based on the fitted extreme value distribution for each genotype separately.