Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays

Petra Matějková; Michal Strouhal; David Šmajs; Steven J Norris; Timothy Palzkill; Joseph F Petrosino; Erica Sodergren; Jason E Norton; Jaz Singh; Todd A Richmond; Michael N Molla; Thomas J Albert; George M Weinstock

doi:10.1186/1471-2180-8-76

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.	ORF^a	Region size (nt)	Size of sequenced region (nt)	Left coordinate^a	Right coordinate^a	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 region^b
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 SNPs^c and 7 variable regions^d		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].

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