We developed VMap 3, the third version of the high-density genetic variation map of wheat by whole-genome sequencing of all species of AA, AABB and AABBDD genomes within the genus Triticum, and the progenitor of D subgenome of bread wheat, Aegilops. tasuschii. There will have serval versions to meet different requirements.
The original version was built using reference IWGSC RefSeq v1.0, aligner Bwa (Version: 0.7.17-r1188) and the SNP caller FastCall 2 (TIGER_v1.0.3.jar). It includes 1196 hexaploid wheat (AABBDD genome), 212 tetraploid wheat (AABB genome), and 220 Ae. tauschii (DD genome). This version keeps both biallelic and triallelic SNPs and Indels that generated 875,151,958 variants totally.
This version goes through the first filtration by the 80% reliable site library. It includes 382,759,847 variants of biallelic and triallelic, both SNPs and Indels.
The second version is based on filtering 80% reliable site library, the following parameters are filtered:
This version reserves 357,231,897 variants, containing biallelic SNPs and Indels.
The third version builds on the second version that only retains 344,460,342 variants of biallelic SNPs.
yf.guo@genetics.ac.cn (Yafei Guo); songxycc@gmail.com (Xinyue Song); flu@genetics.ac.cn (Fei Lu)
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences