Genotype-be-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 <i>Micropterus floridanus</i> genome. Individuals include northern Largemouth Bass (<i>M. salmoides</i>), largemouth bass from the Mobile-Tensaw delta, Florida Bass (<i>M. floridanus</i>), 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 &lt;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 &gt; 0.2) or within the same 1000‐bp window were pruned using BCFtools.