TABLE 3.
SNPs detected within patient specimen sets
| Patient specimen seta | Gene containing within-host SNPs | No. of SNPs | Genome location(s) (SNP and nucleotide coverage for each variant) | Reference genome used forcalling the SNPsb |
|---|---|---|---|---|
| 107R and 107V | Gene for hypothetical protein (FSW4_RS00260) | 1 | 54906 (C→T; T:62, C:1) | F/SW4 (NC_017951.1) |
| Gene for hypothetical protein (FSW4_RS00270) | 2 | 59520 (T→C; C:33, T:0), 59523 (C→T; T:33, C:0) | F/SW4 (NC_017951.1) | |
| Intergenic region | 1 | 79002 (G→A; A:77, G:0) | F/SW4 (NC_017951.1) | |
| Gene for amino acid ABC transporter ATP-binding protein | 1 | 146249 (C→T; T:145, C:0) | F/SW4 (NC_017951.1) | |
| Intergenic region | 1 | 437237 (T→C; C:36, T:0) | F/SW4 (NC_017951.1) | |
| 192R and 192V | Gene for PTS sugar transporter subunit IIA | 1 | 326567 (G→A; A:75, G:5) | F/SW4 (NC_017951.1) |
| 72R and 72V | ompA | 2 | 779230 (G→A; A:33, G:1), 779235 (C→A; A:31, G:2) | D/UW-3/CX (NC_000117.1) |
| Gene for hypothetical protein (CT_744) | 1 | 864903 (T→C; C:50, T→0) | D/UW-3/CX (NC_000117.1) | |
| pmpF | 2 | 1029641 (G→T; T:75, G:0), 1029643 (A→G; G:75, A:0) | D/UW-3/CX (NC_000117.1) | |
| 98R and 98V | Gene for hypothetical protein (CT_049) | 1 | 54281 (C→T; T:23, C:0) | D/UW-3/CX (NC_000117.1) |
a
R, rectal; V, vaginal.
b
SNPs were called by comparing the genomes of patient specimen sets to reference genomes that clustered in the whole-genome phylogenetic tree.