SNP calling
All quality-filtered reads were mapped to the Syngnathus scovellireference genome using BWA-MEM with the parameters aln −e 10 −t 4 −l 32
−i 15 −q 10 (Li & Durbin 2009). The alignment files were imported to
SAMtools for sorting and removal of duplicated reads (Li 2011).
Sequencing coverage and depth for each sample were calculated. SNPs were
detected using SAMtools and then filtered to meet the following
criteria: (1) quality score ≥ 20, (2) coverage depth ≥ 5 and ≤ 1000, (3)
SNPs with minor allele frequency (MAF) > 0.01, and (4) a
missing ratio of samples within each group < 50%.