Abstract: A method for low frequency somatic cell mutation identification and quantification, relating specifically to a method for transposon copy number and genome location identification. Specific sites of different transposon families are used, transposon insertion sequences are specifically enriched via library construction, high-throughput sequencing and bioinformatics analysis are used, and genome locations, copy numbers and types of transposons within samples are accurately identified. The method economically and accurately identifies copy numbers and genome locations of transposons.