We estimated the genotype likelihood (GL) for each site using the option “-GL 3” (SOAPsnp model) implemented in angsd 0.700 . We also performed SNP calling using the HaplotypeCaller in the Genome Analysis Toolkit (GATK) V-3.4-46 . Default options of GATK and the “-rf BadCigar” options were used. SNPs were filtered for low missing rate < 5% and a mean depth ≥ 4. The complete script from the raw data to the GL or SNP data analysis is available as a Additional file 1: Table S1.