Table 3 Summary of cotton base variations
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%) |