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Based on the characteristics of the whole genome sequence of Mycoplasma pneumoniae, Qikai Gene used an autonomous probe design platform to cover the full length of the genome and the polymorphic loci of its isolates with tiled probes. Qikai Gene matching hybridization capture kit combined with high-throughput sequencing was used to launch a complete solution for the whole genome capture of Mycoplasma pneumoniae. It will help to trace the origin and evolution of mycoplasma pneumoniae and other epidemiological studies to provide strong evidence for timely prevention and control.