Basic Info

Defining Mycoplasma Pneumoniae lineages based on variation site information from four lineages

More Details

Using Snippy v4.6.0 software, align the uploaded sequence with the reference genome of Mycoplasma pneumoniae M129-B7 (CP003913.2). Subsequently, convert the alignment results into VCF (Variant Call Format) using the faToVcf tool. Utilize vcftools v0.1.16 software to filter and identify variant information specific to the 86 genotyping variation sites that distinguish the four Mycoplasma pneumoniae lineages: T1-2, T1-3-R, T2-A, and T2-B. Determined phylogenetic lineage of the uploaded sequence based on SNP profiles.

What's New

NA

Additional Information

Related links:

https://vcftools.github.io/

http://hgdownload.soe.ucsc.edu/admin/exe/

https://github.com/tseemann/snippy

Literature

Sun Y, Li P, Jin R, Liang Y, Yuan J, Lu Z, et al. Characterizing the epidemiology of Mycoplasma pneumoniae infections in China in 2022–2024: a nationwide cross-sectional study of over 1.6 million cases. J Abbrev. 2025;14(1).doi: 10.1080/22221751.2025.2482703.