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).