Table 2 Table with the number of variants (SNPs and InDels), variants’ rate, and density, after filtration with the filters suggested by27. Rate is the mean of base pairs in which one variant occurs, and density considers the mean of variants that occur in a window of 1 kbp. All are based on chromosome size (sequencing data).
From: Whole-genome polymorphisms and relatedness of rice varieties circulating in the Mediterranean market
Chromosome | SNPs | InDels | Variant rate | Variant density |
|---|---|---|---|---|
1 | 373,875 | 124,921 | 86.73 | 11.53 |
2 | 321,282 | 105,693 | 84.21 | 11.88 |
3 | 301,230 | 97,679 | 90.72 | 11.02 |
4 | 317,190 | 111,756 | 82.74 | 12.09 |
5 | 231,834 | 76,003 | 96.59 | 10.35 |
6 | 341,719 | 109,188 | 68.15 | 14.67 |
7 | 292,218 | 101,529 | 75.29 | 13.28 |
8 | 298,950 | 100,276 | 71.22 | 14.04 |
9 | 213,904 | 71,835 | 79.42 | 12.59 |
10 | 273,904 | 88,746 | 62.70 | 15.95 |
11 | 365,425 | 126,551 | 57.64 | 17.35 |
12 | 281,447 | 102,941 | 71.70 | 13.95 |
All | 3,612,131 | 1,217,118 | 76.77 | 13.03 |
