clone_jzg22

This script we used for jzg population analysis with 2022 refenrence data

01 build the reference genome

Scripts we used for build the reference are in 01_ref.

02 check clone

Scripts we used for checking clone and call variants are in 02_check_clone.

03 estimate population age

Scripts we uesd for estimating the T. latifolia clonal population age in 03_estimate_population_age.

04 clonal development routes

Scripts we uesd for build the clonal phylogenetic tree, and map the tree to the geographic locations in 04_clonal_development_routes.

05 characteristic of somatic mutations

Scripts we uesd for checking position, direction of somatic mutations. meanwhile, check the non-synonymous mutation site during the development and the vaf of somatic mutations in 05_position_direction_vaf.

06 data

Files that we used as material or the file lists we used for analysis are in data.