Table 1.
Variant calling statistics, considering strain-specific reads and considering total reads produced
| Isolate | INRA-156 | INRA-159 | INRA-164 | INRA-171 | INRA-181 | INRA-195 | Totala |
|---|---|---|---|---|---|---|---|
| % of reference genome callableb | 97.7% | 97.7% | 97.6% | 97.6% | 97.5% | 97.7% | 98.3% |
| Number of SNPs | 144,679 | 146,849 | 144,802 | 143,283 | 145,071 | 145,840 | 234,151 |
| Number of InDels | 4,929 | 5,073 | 4,953 | 4,844 | 4,938 | 4,970 | 8,605 |
| Total number of variants | 149,608 | 151,922 | 149,755 | 148,127 | 150,009 | 150,810 | 242,756 |
| Mean depth of sequencing at variant position (X) | 72.3 | 83.5 | 78.0 | 79.5 | 79.6 | 80.3 | 78.9 |
| Mean variant density (variants per kb) | 3.9 | 4.0 | 3.9 | 3.9 | 3.9 | 4.0 | 6.4 |
| Number of exonic variants | 70,850 | 71,488 | 70,259 | 69,130 | 70,659 | 71,676 | 111,975 |
| Number of intronic variants | 10,779 | 10,821 | 10,509 | 10,320 | 10,682 | 10,786 | 17,095 |
| Number of non-genic variants | 67,979 | 69,613 | 68,987 | 68,677 | 68,668 | 68,348 | 113,686 |
| Number of variants with French genomes | 66,726 | 69,040 | 66,873 | 65,245 | 67,127 | 67,928 | 159,874 |
a: considering all reads produced by whole genome sequencing of the six isolates
b: exluding the end of the chromosome IV from 7,953,943 bp onwards, corresponding to repeated RNA encoding sequence (see Methods)