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Table 1 SNP and individual filtering procedure

From: Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing

Filtering step Number of SNPs eliminated Number of SNPs remaining Number of individuals eliminated Number of individuals remaining
Raw RAD-Seq processing 0 28,415 0 96
Missing Genotypes 14,778 13,637 0 96
SNPs (> 50%)
Missing Genotypes 0 13,637 15 81
Individuals (> 25%)
Excess heterozygosity 4,895 8,742 0 81
(PSVs; > 70%)
Mendelian errors 485 8,257 0 81
SNPs (≥ 2)
Mendelian errors 0 8,257 4 77
Individuals (> 200)
  1. Stringent quality control filtering was applied to the initial set of 28,415 putative SNPs generated from the raw RAD-Seq reads. Filtering parameters for SNPs included removing excess missing data (> 50%), excess Mendelian errors (≥ 2 individuals) and excess heterozygosity (putative PSVs; > 70%). The final number of SNPs left for linkage map construction was 8,257. Individuals were removed if they showed excess missing genotypes (> 25% of the SNPs) and/or excess Mendelian errors (> 200 SNPs). 77 individuals remained for linkage map construction post-filtering.