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

BMC Genomics

Table 1 SNP and individual filtering procedure

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%)	14,778	13,637	0	96
Missing Genotypes	0	13,637	15	81
Individuals (> 25%)	0	13,637	15	81
Excess heterozygosity	4,895	8,742	0	81
(PSVs; > 70%)	4,895	8,742	0	81
Mendelian errors	485	8,257	0	81
SNPs (≥ 2)	485	8,257	0	81
Mendelian errors	0	8,257	4	77
Individuals (> 200)	0	8,257	4	77

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.

ISSN: 1471-2164