Calculated Dn/Ds values for genes from 372 genomes of Mycobacterium tuberculosis (Beijing genotype)

Dn/ds ratio was calculated as described by Nei and Gojobori. All genomes were downloaded from SRA archive NCBI then these data were mapped on the reference genome M. tuberculosis H37Rv (NC_000962.3) and held SNP-calling by samtools. The created vcf files were analyzed and calculated the number of synonymous and non synonymous SNPs for each gene in genome. After that sequences were created for each gene with detected mutations and were compared with reference genome

该比率（Dn/ds）的计算方法遵循了Nei和Gojobori的描述。所有基因组数据均从NCBI的SRA档案中下载，随后这些数据被映射至参考基因组M. tuberculosis H37Rv（NC_000962.3）。通过samtools进行了单核苷酸多态性（SNP）的鉴定。生成的vcf文件经过分析，计算了基因组中每个基因的同义与非同义SNP数量。随后，对于每个检测到突变的基因，创建了序列，并与参考基因组进行了比对。