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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
  1. aThe 261 G. barbadense accessions were aligned to the “TM-1” reference genome. The G. barbadense population SNP and InDel calling results against the “3–79” reference genome are shown in Additional file 1: Table S5. bGenotyping structural variations (SVs) in 742 cottons. The G. hirsutum TM-1 reference genome was used for detecting variations. The number of genotypes in each group is in parentheses. “NA” represents the missing combined SVs. DUP, INV, and TRA were not included for the GhImpCHN population. cCNVs were identified in 742 cottons. Only variation in each chromosome was counted and further analyzed