Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing

Rice

Table 1 Summary of the total variations (SNPs/indels) detected in the germplasm and subgroups and the location distribution of the variations

^aHQ variation: High-quality variation, referring to variations excluding missing genotypes and MAF ≥ 0.01
^bSubgroups in the whole collection. The numbers in brackets indicate the number of accessions
^cThree mixed accessions belong to Group III, IV and V in the 50 cultivated and wild rice group were excluded here
^dThe genic region also includes tRNAs and rRNAs. ^cThe total number of genes that the variations harbored