Filter # SNPs remaining after filtering # SNPs remaining after filtering
S. umbilicalis N. lapillus
Stacks catalogue 2,494,940 2,325,766
SNPs in >75% populations 2,494,940 2,325,766
SNPs with mean depth >10 1,438,613 154,624
SNPs with <20% missing data 121,613 29,287
SNPs with average MAF >0.05 15,682 5,529
SNPs with LD r2 < 0.7 11,601 3,856
SNPs in HWE in at least 60% populations 11,600 3,844