Black grouse autosome consensus sequence

Black grouse autosome consensus sequence used as input for PSMC. The file was generated from a filtered bam file using the samtools mpileup, bcftools and vcfutils.pl (vcf2fq) pipeline (downgrading mapping quality for reads containing excessive mismatches (-C) to 50, minimum read depth (-d) set to 1/3 of the mean genome coverage (28) and maximum read depth (-D) set to twice the mean genome coverage (171)). All non-autosomal sites were discarded.

用作PSMC分析输入的黑琴鸡常染色体一致序列。该文件通过经过滤处理的BAM（Binary Alignment Map，二进制比对映射文件），借助samtools mpileup、bcftools与vcfutils.pl（vcf2fq）分析流程生成：将携带过量错配的读段的比对质量值（-C参数）下调至50，最小读取深度（-d参数）设置为平均基因组覆盖度的1/3（对应数值28），最大读取深度（-D参数）设置为平均基因组覆盖度的2倍（对应数值171）。所有非常染色体位点均被剔除。