mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_vch_pgi | 526,792 | 0 | A | C | 33.3% | 37.6 / 25.6 | 42 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_vch_pgi | 4,296,063 | 0 | C | T | 31.4% | 57.1 / 30.7 | 51 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_vch_pgi | 526,796 | 0 | C | G | 30.9% | 58.4 / 35.4 | 42 | A1179G (GCG→GGG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_vch_pgi | 526,800 | 0 | A | G | 30.8% | 54.0 / 21.0 | 40 | E1180E (GAA→GAG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_vch_pgi | 1,932,094 | 0 | C | G | 25.9% | 33.8 / 16.2 | 27 | intergenic (+35/+21) | purT/eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| * | NC_000913_3_vch_pgi | 1,932,095 | 0 | T | A | 25.9% | 38.1 / 13.7 | 27 | intergenic (+36/+20) | purT/eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| * | NC_000913_3_vch_pgi | 1,932,096 | 0 | C | G | 25.0% | 41.5 / 15.2 | 28 | intergenic (+37/+19) | purT/eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| * | NC_000913_3_vch_pgi | 543,091 | 0 | G | C | 23.8% | 30.6 / 11.5 | 23 | intergenic (+58/+170) | glxK/allE | glycerate kinase II/S‑ureidoglycine aminohydrolase |
| Marginal new junction evidence (lowest skew 10 of 26 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_vch_pgi | 4094416 = | 51 (1.610) | 5 (0.160) | 5/282 | 3.7 | 9.9% | noncoding (101/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913_3_vch_pgi | 4094622 = | 41 (1.320) | noncoding (307/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | NC_000913_3_vch_pgi | = 2074690 | 41 (1.300) | 5 (0.170) | 4/264 | 3.9 | 11.8% | intergenic (+32/‑89) | flu/yeeR | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter/CP4‑44 prophage; putative membrane protein |
| ? | NC_000913_3_vch_pgi | = 2074691 | 37 (1.280) | intergenic (+33/‑88) | flu/yeeR | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter/CP4‑44 prophage; putative membrane protein | |||||
| * | ? | NC_000913_3_vch_pgi | = 3530670 | 36 (1.140) | 4 (0.140) | 4/268 | 4.0 | 10.9% | intergenic (+18/+45) | hslO/yhgE | heat shock protein Hsp33/DUF4153 family putative inner membrane protein |
| ? | NC_000913_3_vch_pgi | = 3530674 | 32 (1.090) | intergenic (+22/+41) | hslO/yhgE | heat shock protein Hsp33/DUF4153 family putative inner membrane protein | |||||
| * | ? | NC_000913_3_vch_pgi | = 1712803 | 25 (0.790) | 4 (0.140) | 4/270 | 4.0 | 14.4% | coding (35/1503 nt) | dtpA | dipeptide and tripeptide permease A |
| ? | NC_000913_3_vch_pgi | = 1712811 | 24 (0.810) | coding (43/1503 nt) | dtpA | dipeptide and tripeptide permease A | |||||
| * | ? | NC_000913_3_vch_pgi | 4296401 = | 32 (1.010) | 4 (0.130) | 4/274 | 4.1 | 10.5% | noncoding (564/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites |
| ? | NC_000913_3_vch_pgi | 4296434 = | 38 (1.260) | noncoding (597/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913_3_vch_pgi | 4094596 = | 48 (1.520) | 4 (0.130) | 4/274 | 4.1 | 8.7% | noncoding (281/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913_3_vch_pgi | 4094626 = | 38 (1.260) | noncoding (311/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | NC_000913_3_vch_pgi | 4094504 = | 42 (1.330) | 4 (0.130) | 4/274 | 4.1 | 9.3% | noncoding (189/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913_3_vch_pgi | 4094626 = | 38 (1.260) | noncoding (311/402 nt) | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | NC_000913_3_vch_pgi | 1457261 = | 41 (1.300) | 4 (0.130) | 4/274 | 4.1 | 9.6% | coding (832/1071 nt) | paaE | ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component |
| ? | NC_000913_3_vch_pgi | 1457296 = | 36 (1.200) | coding (867/1071 nt) | paaE | ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component | |||||
| * | ? | NC_000913_3_vch_pgi | 1027524 = | 29 (0.920) | 4 (0.130) | 4/278 | 4.1 | 12.5% | coding (250/663 nt) | yccT | UPF0319 family protein |
| ? | NC_000913_3_vch_pgi | 1027537 = | 28 (0.920) | coding (237/663 nt) | yccT | UPF0319 family protein | |||||
| * | ? | NC_000913_3_vch_pgi | = 3867983 | 31 (0.980) | 4 (0.130) | 4/282 | 4.2 | 11.2% | coding (256/333 nt) | yidQ | DUF1375 family outer membrane protein |
| ? | NC_000913_3_vch_pgi | = 3868014 | 33 (1.070) | coding (287/333 nt) | yidQ | DUF1375 family outer membrane protein | |||||