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

Table 2 SNP filtering criteria for SNP discovery

Criteria used for SNP calling	Cut-off values
Minimum mapped read depth to the reference	≥ 3
Maximum mapped read depth to the reference	$\bar{X}$ + 2s^a
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

^a $\bar{X}$ + 2s is the average read depth and standard deviation estimated based on the fitted extreme value distribution for each genotype separately.