3.3 Individual whole-genome resequencing
Between 21 and 27 giga base pairs (Gb) of sequencing data, corresponding to over 150 million reads mapped as pairs to the Salmo trutta reference genome per Lakes Bunnersjöarna individual (Table S5). This corresponds to approximately 98% of the raw data per individual. An average mapping quality of 32 and depth of coverage c. 10X was observed (Tables S5). In total, 21 million variants were called of which c. 20 million variants were retained after hard filtering. After removing indels, while keeping only bi-allelic SNPs with minor allele frequency (MAF)≥0.01 assigned to any of the 40 S. trutta chromosomes, c. 10 million SNPs were retained and were used for ROH estimation. Similar results were obtained from individual WGS from other lakes (Table S6).