2.3 Reads mapping and SNP calling
Raw sequence reads were mapped to the M. alternatus reference
genome using the Burrows–Wheeler Aligner (BWA) with the command ‘mem -t
4 -k 32 –M’ (Li & Durbin, 2009). To reduce mismatches generated by PCR
amplification before sequencing, duplicated reads were removed with
SAMtools (Li et al., 2009). After alignment, SNP calling was performed
on a population scale using a Bayesian approach as implemented in the
package SAMtools, and then genotype likelihoods from reads for each
individual at each genomic location and the allele frequencies in the
sample were calculated with a Bayesian approach. The ‘mpileup’ command
was used to identify SNPs with the parameters as ‘-q 1 -C 50 -t SP -t DP
-m 2 -F 0.002’. Specifically, a SNP was retained when it met the
following criteria: coverage depth ≥2 and ≤30, minor allele frequency
(MAF) ≥0.05, MISS ≤0.1.