Table 1.
DDT sequencing of 38 hypervariable regions where SNPs could not be identified by CGS
| Region no. | ORFa | Region size (nt) | Size of sequenced region (nt) | Left coordinatea | Right coordinatea | Newly found changes in the regions suggested by CGS | Newly found changes not suggested by mapping phase of CGS | Confirmation of SNPs identified by CGS in this regionb |
| 1 | TP0012 | 37 | 390 | 12322 | 12711 | 3 nt deletion | - | - |
| 2 | TP0076 | 29 | 529 | 83788 | 84316 | - | 1 solitary SNP | - |
| 3 | TP0117 | 86 | 699 | 134808 | 135506 | 7 clustered SNPs | - | - |
| 4 | TP0117 | 86 | 3 clustered SNPs | - | - | |||
| 5 | TP0126 | 29 | 393 | 147948 | 148340 | 1 solitary SNP | - | - |
| 6 | upstream | 29 | 460 | 149103 | 149562 | 2 clustered SNPs | - | - |
| of TP0128 | 1 nt + 5 nt insertions | |||||||
| 7 | TP0131 | 421 | 723 | 150925 | 151647 | 3 clustered SNPs, 1 solitary SNP | 2 clustered SNPs | - |
| 8 | upstream of TP0136 | 29 | 404 | 156348 | 156751 | 64 nt deletion | - | - |
| 9 | TP0136 | 1087 | 1609 | 156752 | 158360 | 19 clustered SNPs | 8 clustered SNPs | 21 SNPs |
| 1 nt + 1 nt + 1 nt + 6 nt deletions | 2 solitary SNPs | |||||||
| 10 | TP0272 | 29 | 480 | 288647 | 289126 | - | - | - |
| 11 | TP0304 | 37 | 466 | 318761 | 319226 | 3 nt deletion | - | - |
| 12 | TP0326 | 79 | 452 | 345605 | 346056 | 8 clustered SNPs | - | 1 SNP |
| 13 | TP0352 | 29 | 465 | 376926 | 377390 | - | - | - |
| 14 | TP0394 | 29 | 505 | 420353 | 420857 | - | - | 1 SNP |
| 15 | TP0431 | 29 | 465 | 458973 | 459437 | - | - | 1 SNP |
| 16 | TP0457 | 29 | 465 | 487935 | 488399 | - | - | - |
| 17 | TP0484 | 29 | 468 | 514441 | 514908 | - | - | - |
| 18 | TP0486 | 29 | 494 | 517297 | 517790 | - | 1 nt insertion, 1 nt deletion | - |
| 19 | TP0493 | 29 | 478 | 529146 | 529623 | - | - | - |
| 20 | TP0515 | 44 | 506 | 555754 | 556259 | 3 clustered SNPs | - | 4 SNPs |
| 21 | TP0544 | 29 | 611 | 585940 | 586550 | 6 nt insertion | - | - |
| 22 | TP0548 | 835 | 1189 | 591557 | 592745 | 22 clustered SNPs | 2 clustered SNPs | 5 SNPs |
| 3 nt + 4 nt + 5 nt insertions | 1 solitary SNP | |||||||
| 23 | TP0577 | 37 | 405 | 628247 | 628651 | 1 solitary SNP | - | - |
| 24 | TP0598 | 29 | 550 | 648851 | 649400 | - | 4 1 nt insertions | - |
| 25 | TP0620–TP0621 | 51 | 3469 | 670958 | 674426 | - | 4 clustered SNPs | - |
| 26 | TP0668 | 37 | 462 | 730080 | 730541 | 6 nt deletion | - | - |
| 27 | TP0699 | 51 | 469 | 766143 | 766611 | 1 solitary SNP | - | - |
| 28 | TP0785 | 29 | 438 | 851631 | 852068 | - | - | - |
| 29 | TP0814 | 29 | 476 | 882990 | 883465 | - | - | - |
| 30 | TP0865 | 29 | 480 | 943847 | 944326 | 3 nt insertion | - | 1 SNP |
| 31 | TP0866 | 29 | 543 | 944677 | 945219 | - | 1 nt insertion | - |
| 32 | TP0868 | 29 | 454 | 947257 | 947710 | 7 nt deletion | - | - |
| 33 | TP0896–TP0898 | 667 | 3038 | 974053 | 977090 | 4 SNPsc and 7 variable regionsd | 1 SNP | |
| 34 | TP0898 | 27 | 416 | 978349 | 978764 | - | - | - |
| 35 | TP0933 | 29 | 164 | 1014034 | 1014197 | - | - | - |
| 36 | TP0973 | 44 | 396 | 1057660 | 1058055 | 1 solitary SNP | - | 1 SNP (igr) |
| 37 | TP1030–TP1031 | 1507 | 402 | 1123660 | 1124061 | 18 clustered SNPs | 1 nt insertion, | 16 SNPs |
| 1775 | 1124256 | 1126030 | 1 solitary SNP | |||||
| 38 | TP1036 | 29 | 550 | 1132558 | 1133107 | - | - | - |
ORF – open reading frame; nt – nucleotide; SNP – single nucleotide polymorphism; igr – intergenic region; aas described in [3]; bSNPs identified using CGS in these regions were verified by DDT sequencing; c two SNPs represent the group of 17 SNPs in non-unique sites, originally excluded from list of total changes; didentified variable regions in TP0897 were identical to the variable regions V1–V7 described previously [22–24].