Summary of Sequencing Statistics
An average of 262.90 million reads were obtained per sample (min: 208.02M, max: 312,93M, std: 25.90M), generating an average coverage of 36.77x (min: 19.19x, max: 42.89x, std: 3.57x). On average, 98.58% of the reads mapped to the reference genome (min: 97.00%, max: 99.06%, std: 0.52%). Mapping quality was consistent between samples, ranging from 56.00 to 56.90 (average: 56.53, std: 0.22). In total, 98.42% of the genome (min: 97.63%, max: 98.66%, std: 0.28%) had a coverage of at least 10x.
12,819,455 SNPs were found for the Bermudian samples. After filtering, 12,053,478 (94.02%) of those SNPs were kept and used for further analysis of selective sweep regions. For the Hawaiian samples, 11,913,016 SNPs were kept. The Bermudian and Hawaiian samples had 9,734,945 of the analysed SNP locations in common. 7,174,074 SNPs were kept after merging with data from wild and domesticated populations for the Chromopainter analyses, due to missing data in the domesticated and Red Junglefowl populations.