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Table 3 Summary of cotton base variations

From: Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping

Types of SNPs Interspecific EST-SNPs Intraspecific EST-SNPs Total
Inter/hemi-SNPs Hemi-SNPs Subtotal 4 5 6 7 ≥8 Subtotal
C → T 265 (26.26%) 1036 (29.21%) 1301 (28.56%) 158 (30.10%) 153 (36.00%) 249 (27.04%) 103 (29.94%) 170 (24.50%) 833 (28.64%) 2134 (28.59%)
G → A 271(26.86%) 981 (27.66%) 1252 (27.48%) 147 (28.00%) 120 (28.24%) 244 (26.49%) 97 (28.20%) 170 (24.50%) 778 (26.74%) 2030 (27.19%)
All transitions 536 (53.12%) 2017 (56.86%) 2553 (56.04%) 305 (58.10%) 273 (64.24%) 493 (53.53%) 200 (58.14%) 340 (48.99%) 1611 (55.38%) 4164 (55.78%)
C → G 74 (7.33%) 282 (7.95%) 356 (7.81%) 40 (7.62%) 12 (2.82%) 61 (6.62%) 17 (4.94%) 47 (6.77%) 177 (6.09%) 533 (7.14%)
A → T 82 (8.13%) 410 (11.56%) 492 (10.80%) 45 (8.57%) 41 (9.65%) 96 (10.42%) 33 (9.59%) 61 (8.79%) 276 (9.49%) 768 (10.29%)
C → A 88 (8.72%) 304 (8.57%) 392 (8.60%) 33 (6.29%) 31 (7.29%) 67 (7.27%) 23 (6.69%) 53 (7.64%) 207 (7.12%) 599 (8.02%)
T → G 97 (9.61%) 304 (8.57%) 401 (8.80%) 42 (8.00%) 32 (7.53%) 79 (8.58%) 19 (5.52%) 73 (10.52%) 245 (8.42%) 646 (8.65%)
All transversions 341 (33.80%) 1300 (36.65%) 1641 (36.02) 160 (30.48%) 116 (27.29%) 303 (32.90%) 92 (26.74%) 234 (33.72%) 905 (31.11%) 2546 (34.11%)
A/- 52 (5.15%) 56 (1.58%) 108 (2.37%) 18 (3.43%) 13 (3.06%) 40 (4.34%) 25 (7.27%) 47 (6.77%) 143 (4.92%) 251 (3.36%)
C/- 22 (2.18%) 36 (1.01%) 58 (1.27%) 13 (2.48%) 5 (1.18%) 29 (3.15%) 4 (1.16%) 16 (2.31%) 67 (2.30%) 125 (1.67%)
G/- 28 (2.78%) 37 (1.04%) 65 (1.43%) 16 (3.05%) 3 (0.71%) 27 (2.93%) 11 (3.20%) 22 (3.17%) 79 (2.72%) 144 (1.93%)
T/- 30 (2.97%) 101 (2.85%) 131 (2.88%) 13 (2.48%) 15 (3.53%) 29 (3.15%) 12 (3.49%) 35 (5.04%) 104 (3.58%) 235 (3.15%)
All InDels 132 (13.08%) 230 (6.48%) 362 (7.95%) 60 (11.43%) 36 (8.47%) 125 (13.57%) 52 (15.12%) 120 (17.29%) 393 (13.51%) 755 (10.11%)
Total 1009 (100.00%) 3547 (100.00%) 4556 (100.00%) 525 (100.00%) 425 (100.00%) 921 (100.00%) 344 (100.00%) 694 (100.00%) 2909 (100.00%) 7465 (100.00%)