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

Table 2 Genotypic differences between shared SNPs from the different pipelines

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

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

ISSN: 1471-2164