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Table 1 DDT sequencing of 38 hypervariable regions where SNPs could not be identified by CGS

From: Complete genome sequence of Treponema pallidum ssp. pallidumstrain SS14 determined with oligonucleotide arrays

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 - - -
  1. 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].