Table 1.
Polymorphism | Total | Isolate | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Acacia | A517 | BO5.10 | 1.01.12 | Grape | GLO1 | Geranium | Katie tomato | Davis navel | Rose | Noble rot | UKR | 1.01.06 | ||
SNPs | 980,329 | 216,299 | 335,768 | 173,741 | 202,270 | 357,305 | 213,332 | 205,957 | 127,779 | 180,103 | 166,813 | 169,336 | 240,348 | 172,830 |
Indels | 157,936 | 28,232 | 39,506 | 20,843 | 26,030 | 46,303 | 28,064 | 24,380 | 16,330 | 22,044 | 21,823 | 19,990 | 29,151 | 22,141 |
Insertions | 87,489 | 15,039 | 20,751 | 10,820 | 13,724 | 25,137 | 14,990 | 12,568 | 8492 | 11,424 | 11,529 | 10,197 | 15,354 | 11,536 |
Deletions | 70,447 | 13,193 | 18,755 | 10,023 | 12,306 | 21,166 | 13,074 | 11,812 | 7838 | 10,620 | 10,294 | 9793 | 13,797 | 10,605 |
Largest insertion | 58 | 58 | 57 | 56 | 58 | 58 | 58 | 56 | 56 | 56 | 57 | 56 | 59 | 56 |
Largest deletion | 74 | 74 | 74 | 72 | 73 | 74 | 73 | 72 | 72 | 73 | 72 | 73 | 72 | 73 |
Change every (bp) | 36 | 170 | 110 | 213 | 182 | 103 | 172 | 180 | 288 | 205 | 220 | 219 | 154 | 213 |
Changes per kb | 28 | 6 | 9 | 5 | 5 | 10 | 6 | 6 | 3 | 5 | 5 | 5 | 6 | 5 |
Missense/Silent | 0.755 | 0.705 | 0.689 | 0.737 | 0.755 | 0.673 | 0.733 | 0.741 | 0.721 | 0.731 | 0.745 | 0.741 | 0.719 | 0.735 |
Missense | 98,400 | 21,831 | 34,264 | 18,091 | 21,529 | 34,489 | 22,031 | 22,285 | 12,807 | 18,700 | 17,589 | 18,049 | 25,784 | 17,916 |
Nonsense | 1255 | 180 | 264 | 126 | 222 | 290 | 157 | 188 | 85 | 155 | 130 | 143 | 216 | 150 |
Silent | 130,295 | 30,950 | 49,709 | 24,562 | 28,535 | 51,215 | 30,066 | 30,096 | 17,766 | 25,577 | 23,596 | 24,355 | 35,839 | 24,393 |
Major effect changes | 5963 | 1113 | 1412 | 717 | 1037 | 1613 | 982 | 877 | 494 | 772 | 848 | 683 | 1090 | 743 |
Sequence depth | 92 | 55 | 46 | 85 | 141 | 78 | 52 | 59 | 52 | 78 | 33 | 13 | 56 |
The total number of genomic polymorphisms per polymorphism type detailed per individual genotype in comparison to the T4 reference genome. The total shows the unique occurrence summation across all genotypes. Largest insertion and deletion are in bp.