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Table 2 Genotypic differences between shared SNPs from the different pipelines

From: Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species

Species SNPs Panel Hom → Hom Hom → MD MD → Hom Het → MD MD → Het Hom → Het Het → Hom
Manila clam COM 0.00062 0.01500 0.01884 0.01324 0.00569 0.00349 0.01333
RG-STA 0.00007 0.01759 0.00217 0.00567 0.00105 0.00336 0.00369
RG-ALT 0.00017 0.01018 0.00450 0.01376 0.00300 0.00150 0.01243
Common cockle COM 0.00004 0.00575 0.00557 0.01145 0.00273 0.00331 0.00475
Brown trout COM 0.00002 0.01285 0.01196 0.00952 0.01161 0.00407 0.00150
RG-STA 0 0.01231 0.00708 0.00944 0.00021 0.00020 0.00744
RG-ALT 0 0.00179 0.00564 0.00780 0.00040 0.00009 0.00060
Silver catfish COM 0.00019 0.00765 0.00520 0.00848 0.00382 0.00349 0.00547
Small-spotted catshark COM 0.00098 0.04128 0.01311 0.05881 0.03522 0.01163 0.01393
  1. Genotyping differences are presented as the relative frequency of total genotypes. COM panels were obtained with shared SNPs between STA and ALT panels (both de novo approach). RG-STA panels were obtained with shared SNPs between RG and STA (reference genome and de novo approach). RG-ALT panels were obtained with shared SNPs between RG and ALT (reference genome and de novo approach). Hom: Homozygous; MD: Missing data (i.e. missing genotype); Het: Heterozygous