Sequence data processing and SNP calling
Raw reads were processed through a series of quality control procedures
which involved; (i) removing reads with ≥10% unidentified nucleotides
(N); (ii) reads with >50% bases with a Phred quality
< 5; (iii) removing reads with >10 nucleotides
alignment to the adapter; (iv) allowing ≤10% mismatches; and (v)
removing reads that contain the Hae III enzyme sequence.
Burrows-Wheeler Aligner (BWA) version 0.7.17 was used to align the
retained reads against the Coturnix Japonica 2.0 genome (Assembly
accession number GCF_001577835.1) with the parameters mem -t 4 -k 32
-M’ (Li & Durbin, 2009). Variant calling was performed using
SAMtools version 1.11mpileup command (Li et al., 2009) in conjunction with
BCFtools
version 1.11 call command
(Li, 2011). Variant filtering was performed by restricting the dataset
to biallelic SNPs found in at least 80% of samples, with a minimum
depth of 2 reads, minimum Phred score of 30, and minimum minor allele
frequency (MAF) of 0.01 using VCFtools version 0.1.13 (Danecek et al.,
2011). Additional filtering was also done using PLINK version 1.9
(Purcell et al., 2007) to remove individuals with missing genotype data
(–mind 0.1), variants with missing genotype data (–geno 0.05),
minor allele frequency threshold (–maf 0.05) and Hardy–Weinberg
exact test threshold (–hwe 1e6).