Table 1 Genome-wide genomic variations in a large cotton population
From: Cotton pan-genome retrieves the lost sequences and genes during domestication and selection
Variation type | Total (1913) | Gh cultivar (1623) | Ghlandrace (256) | GhImpUSO (438) | GhImpCHN (929) | Gb cultivar (261) | AD3-AD7 (26) |
|---|---|---|---|---|---|---|---|
Bi-allele SNPa | 19,246,497 | 9,546,748 | 9,265,438 | 4766,399 | 3,761,448 | 19,473,033 | 32,878,758 |
Splicing | 2172 | 1213 | 1149 | 652 | 554 | 2041 | 11,366 |
Exonic | 315,404 | 179,665 | 172,718 | 103,126 | 89,208 | 316,146 | 776,644 |
Intronic | 607,301 | 335,212 | 322,141 | 189,798 | 152,656 | 575,524 | 1,010,509 |
UTR | 220,664 | 120,198 | 116,269 | 65,226 | 52,342 | 197,420 | 390,008 |
Upstream | 869,678 | 448,709 | 432,640 | 238,937 | 169,788 | 789,898 | 984,811 |
Downstream | 797,469 | 413,937 | 399,140 | 222,266 | 161,602 | 729,445 | 959,584 |
Nonsynonymous | 195,883 | 111,686 | 107,143 | 63,008 | 52,853 | 177,474 | 420,190 |
InDel (≤ 20 bp) a | 4,815,125 | 3,971,277 | 3,744,299 | 1,672,195 | 1,726,445 | 3,366,481 | 7,625,077 |
Splicing | 1202 | 1128 | 941 | 570 | 735 | 1104 | 2465 |
Exonic | 31,661 | 27,238 | 28,815 | 12,807 | 14,826 | 26,455 | 65,677 |
Intronic | 262,657 | 231,561 | 215,663 | 95,674 | 94,830 | 183,387 | 539,379 |
UTR | 113,824 | 100,811 | 96,003 | 36,418 | 37,175 | 76,684 | 261,351 |
Upstream | 578,086 | 497,660 | 413,192 | 201,122 | 226,848 | 400,965 | 927,134 |
Downstream | 429,514 | 369,517 | 311,164 | 148,050 | 166,059 | 309,829 | 717,980 |
Frameshift | 23,330 | 20,367 | 22,040 | 9798 | 11,029 | 19,603 | 42,328 |
SV (> 50 bp) | 214,310 | 104,523 | 97,933 | 64,064 | 61,616 | 132,499 | 281,476 |
Deletionb | 32,099 | 22,340 | 9933 | 7029 | 23,559 | 13,982 | 15,484 |
Duplicationb | 7576 | 5146 | 4766 | 1721 | NA | 3252 | 3718 |
Inversionb | 1112 | 724 | 615 | 310 | NA | 877 | 613 |
Translocationb | 357 | 240 | 188 | 167 | NA | 504 | 412 |
CNVc | 173,166 | 76,073 | 82,431 | 54,837 | 38,057 | 99,274 | 261,249 |