Genotype-by-sequencing SNPs for three largemouth bass lineages and hybrids

8,582 SNPs across 144 largemouth bass individuals, derived by genotype-by-sequencing with PstI enzyme. GBS data was assembled with Stacks2 and a draft Micropterus floridanus genome. Individuals include northern Largemouth Bass (M. salmoides), largemouth bass from the Mobile-Tensaw delta, Florida Bass (M. floridanus), and intergrades. Filtering: Biallelic SNPs were retained if they had a minor allele frequency greater than 0.05, had a minor allele count greater than 4, were genotyped in at least three population groups (NLB, DLB, FLB, or ILB), and had <15% missing data across all individuals. SNPs that departed Hardy–Weinberg equilibrium with a p‐value cutoff of 0.05 in two or more sampling sites were also removed. SNPs in linkage disequilibrium (r2 > 0.2) or within the same 1000‐bp window were pruned using BCFtools.
File NFLDB_popname.strata has population info for samples. NB=Northern Largemouth Bass, DB=Delta Largemouth Bass, FB=Florida Bass, ILMB=Intergrade largemouth bass