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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].
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BMC Microbiology

ISSN: 1471-2180

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