Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

BMC Bioinformatics

Table 2 Single-nucleotide polymorphisms identified by Not-N analysis for the major subtypes of hepatitis C virus.

HCV subtype^a	No. genotypes	SNP 1		SNP 2
		Position^b	Discrimination (%)	Position	Discrimination (%)
1a	117	126* (C or T)	100	-	-
1b	382	103 (C)	72.1	194* (G)/238* (C) 100%	100
2a	38	258 (A or G) 99.7%	99.7	182* (T)	100
2b	53	314 (A)	99.7	127 (A)	100
2c	5	50 (T)	99.7	39* (G)	100
3a	49	295 (G)	100	-	-
3b	6	307 (T)	99.8	126* (G)	100
4a	26	182* (A)	97.8	325* (A)	100
4d	17	154 (A)	100	-	-
4f	21	325* (C)	99.5	194* (T)/238* (A) 100%	100
4t	4	338/339 (C)	100	-	-
5a	18	100 (C)	100	-	-
6a	34	39* (C or T)	100	-	-

^aSubtypes containing less than four confirmed sequences were not included in the analysis. Sequences were downloaded from the hepatitis C virus (HCV) sequence database [10].
^bThe single-nucleotide polymorphism (SNP) position refers to a 340 bp fragment of the RNA-dependent RNA polymerase NS5B spanning nucleotides 8276 to 8615 (GenBank accession AF009606 [48]). NS5B is used to construct phylogenetic trees for HCV, which form the basis of the genotype and subtype nomenclature [40].
*SNP discriminates multiple subtypes.

ISSN: 1471-2105