Table 1 Summary statistics for SNPs and indels among 24 lines of cotton derived from different DNA templates.
DNA template | Primer pairs designed | Amplified primer pairs (%) | Single-copy loci (%)1 | Polymorphic SNP loci (%)2 | SNPs | SNPs/locus1 | bp/SNP2,3 | Polymorphic indel loci (%)2 | Indels | Indels/locus | bp/indel2,3 |
|---|---|---|---|---|---|---|---|---|---|---|---|
EST 3' end | 160 | 102 (64) | 45 (28,44) | 30 (67) | 144 | 3.2 | 252 | 14 (31) | 49 | 1.1 | 741 |
EST 5' end | 988 | 802 (73) | 417 (42,52) | 142 (34) | 417 | 1.0 | 807 | 37 (9) | 109 | 0.3 | 3,087 |
COS | 576 | 523 (91) | 201 (35,38) | 56 (28) | 296 | 1.5 | 548 | 20 (10) | 70 | 0.3 | 2,317 |
Intron | 126 | 98 (78) | 44 (35,45) | 17(39) | 46 | 1.0 | 772 | 11 (25) | 32 | 0.7 | 1,110 |
GSP | 48 | 29 (60) | 23 (48,79) | 11 (48) | 40 | 1.7 | 464 | 5 (22) | 12 | 0.5 | 1,547 |
SSR | 52 | 46 (88) | 21 (40, 46) | 14 (67) | 62 | 3.0 | 273 | 5 (24) | 7 | 0.3 | 2,421 |
BAC | 24 | 7(29) | 0 (0,0) | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a |
Total | 1,974 | 1,607 (81) | 751 (47) | 270 (36) | 1,005 | 1.3 | 603 | 92 (12) | 279 | 0.4 | 2,172 |