Table 2 SNP and Indel variation in cultivated B. vulgaris. Gene diversity (2pq) indicates the diversity and expected genetic variation within populations
Grouping | Accession | Entry | Variation Detected | Lineage-specific Variation | Gene diversity | ||||
|---|---|---|---|---|---|---|---|---|---|
Total variants | SNP variants | Indel variants | Total variants | SNP variants | Indel variants | 2pq | |||
Sugar Beet | EL10 | 1 | 221,493 | 204,260 | 17,233 | 1,149 | 689 | 460 | 0.027 |
C869 | 2 | 3,479,100 | 3,147,716 | 331,384 | 9,514 | 8,290 | 1,224 | 0.194 | |
EL50 | 3 | 4,226,613 | 3,805,108 | 421,505 | 30,712 | 27,667 | 3,045 | 0.159 | |
EL51 | 4 | 4,222,688 | 3,808,158 | 414,530 | 17,464 | 15,547 | 1,917 | 0.195 | |
GP10 | 5 | 4,070,438 | 3,689,994 | 380,444 | 9,051 | 7,999 | 1,052 | 0.230 | |
GP9 | 6 | 4,216,268 | 3,803,842 | 412,426 | 6,094 | 5,366 | 728 | 0.253 | |
L19 | 7 | 3,492,804 | 3,185,964 | 306,840 | 19,938 | 17,854 | 2,084 | 0.187 | |
SP7322 | 8 | 4,295,147 | 3,881,458 | 413,689 | 15,528 | 13,942 | 1,586 | 0.213 | |
SR102 | 9 | 4,052,933 | 3,675,246 | 377,687 | 8,765 | 7,846 | 919 | 0.232 | |
SR98 | 10 | 4,097,388 | 3,702,432 | 394,956 | 16,241 | 14,612 | 1,629 | 0.202 | |
Table Beet | BBTB | 11 | 4,548,634 | 4,064,552 | 484,082 | 88,129 | 79,236 | 8,893 | 0.087 |
Crosby | 12 | 4,553,826 | 4,112,797 | 441,029 | 21,882 | 19,436 | 2,446 | 0.198 | |
DDRT | 13 | 4,526,694 | 4,081,640 | 445,054 | 24,180 | 21,592 | 2,588 | 0.185 | |
RQ | 14 | 4,465,888 | 4,011,300 | 454,588 | 31,786 | 28,714 | 3,072 | 0.154 | |
TG | 15 | 4,066,177 | 3,655,695 | 410,482 | 37,213 | 33,887 | 3,326 | 0.103 | |
W357B | 16 | 4,096,676 | 3,674,030 | 422,646 | 81,786 | 74,941 | 6,845 | 0.043 | |
WT | 17 | 4,440,187 | 3,995,032 | 445,155 | 30,371 | 27,613 | 2,758 | 0.159 | |
Fodder Beet | MAM | 18 | 3,366,421 | 3,087,403 | 279,018 | 11,969 | 10,716 | 1,253 | 0.221 |
WGF | 19 | 4,286,092 | 3,887,565 | 398,527 | 25,210 | 22,850 | 2,360 | 0.202 | |
Chard | FGSC | 20 | 5,355,215 | 4,845,307 | 509,908 | 31,764 | 28,455 | 3,309 | 0.241 |
LUC | 21 | 5,228,873 | 4,745,987 | 482,886 | 35,097 | 31,341 | 3,756 | 0.240 | |
RHU | 22 | 4,500,515 | 4,079,774 | 420,741 | 29,089 | 26,138 | 2,951 | 0.195 | |
Vulcan | 23 | 4,852,749 | 4,378,335 | 474,414 | 37,056 | 33,650 | 3,406 | 0.190 | |
Crop Type | Sugar (Entries 1-10) |  | 9,015,627 | 8,022,713 | 992,914 | 3,659 | 3,317 | 342 | 0.207 ± 0.002 |
Table (Entries 11-17) |  | 8,871,075 | 7,875,142 | 995,933 | 1,937 | 1,379 | 558 | 0.147 ± 0.044 | |
Fodder (Entries 18-19) |  | 5,422,289 | 4,920,209 | 502,080 | 848 | 643 | 205 | 0.221 ± 0.013 | |
Chard (Entries 20-23) |  | 8,684,866 | 7,788,799 | 896,067 | 4,217 | 3,359 | 858 | 0.216 ± 0.027 | |
B. vulgaris (cultivated) | B. vulgaris (SamTools) |  | 14,598,354 | 12,411,164 | 2,187,190 | n/a | n/a | n/a | 0.182 ± 0.040 |
B. vulgaris (GATK) |  | 4,180,197 | 3,809,937 | 370,260 | n/a | n/a | n/a | 0.178 ± 0.060 | |