Table 2.

Deletion Screen of BCG Pasteur Shows that TSTEP/Deletion Assembly Finds Known Deletions plus Three New Deletions

Complete TSTEP/deletion assembly results for screen of BCG Pasteur		RD number		Sequencing confirmation results
Start				Sequencing confirmation results		End		Length		No. of probe pairs	Proportion of probe pairs above the cutoff pvalue
Start						End		Length		No. of probe pairs	Proportion of probe pairs above the cutoff pvalue
Confirmation result	Start	End	Length
264681	266633	1953	35	0.03	RD4	Deletion	264752	266658	1907
1058107	1058601	495	16	0.19		Present
1333051	1334446	1396	29	0.03	N-RD18	Deletion	1332920	1334466	1547
1402897	1405631	2735	51	0.08	RD10	Deletion	1402932	1405939	3008
1483164	1483836	673	13	0.15		Present
1695829	1708776	12948	430	0.04	RD6	Deletion	1696017	1708750	12734
1779216	1789408	10193	380	0.03	RD3	Deletion	1779276	1788525	9250
1998716	2007316	8601	210	0.02	RD14	Deletion	1998225	2007297	9073
2196766	2197597	832	23	0.09		Present
2208107	2231883	23777	705	0.06	RD2, RD15	Deletion	2208003	2231848	23846
2329435	2332234	2800	58	0.05	RD12	Deletion	2330073	2332104	2032
2626662	2637681	11020	271	0.04	RD7	Deletion	2626070	2635032	8963
2969694	2980802	11109	310	0.07	RD13	Deletion	2969988	2981195	11208
3485154	3487575	2422	98	0.05	RD5	Deletion	3484737	3487512	2776
3842882	3846520	3639	119	0.05	RD11	Deletion	3842653	3847540	4888
3896832	3897792	961	27	0.11	N-RD17	Deletion	3897069	3897783	715
4056690	4062741	6052	108	0.03	RD9	Deletion	4056837	4062732	5896
4188975	4190798	1824	29	0.17	N-RD25	Deletion	4189605	4190757	1153
4349983	4359538	9556	127	0.03	RD1	Deletion	4350262	4359720	9459

(TSTEP) Tandom Set Terminal Extreme Probability.
↵After the deletion naming convention in Behr et al. (1999). New deletions are indicated with N-RD.

Detection of Deleted Genomic DNA Using a Semiautomated Computational Analysis of GeneChip Data