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 (highest frequency 20 of 54 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 11,387 | 0 | C | T | 74.2% | 138.6 / 62.5 | 89 | D134N (GAC→AAC) | yaaI | DUF2541 domain‑containing protein YaaI |
| * | NC_000913 | 2,183,816 | 0 | T | C | 73.2% | 195.6 / 72.3 | 108 | Q234R (CAG→CGG) | thiD | bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase |
| * | NC_000913 | 2,695,578 | 1 | . | G | 71.9% | 147.6 / 57.9 | 57 | intergenic (‑35/‑223) | purL/mltF | phosphoribosylformylglycinamide synthetase/membrane‑bound lytic murein transglycosylase F |
| * | NC_000913 | 1,598,040 | 0 | A | G | 68.0% | 143.1 / 85.0 | 100 | pseudogene (47/5422 nt) | yneO | AIDA‑I family autotransporter YneO |
| * | NC_000913 | 2,511,478 | 0 | A | G | 67.5% | 112.9 / 69.3 | 83 | L410P (CTG→CCG) | mntH | Mn(2(+))/Fe(2(+)): H(+) symporter MntH |
| * | NC_000913 | 838,384 | 0 | G | A | 64.6% | 116.6 / 137.2 | 130 | R25C (CGC→TGC) | ybiI | zinc finger domain‑containing protein YbiI |
| * | NC_000913 | 2,381,886 | 0 | T | C | 52.9% | 18.1 / 114.6 | 85 | G93G (GGT→GGC) | rbn | ribonuclease BN |
| * | NC_000913 | 2,047,364 | 0 | T | C | 49.5% | 10.6 / 155.4 | 102 | S809S (AGT→AGC) | yeeJ | inverse autotransporter adhesin |
| * | NC_000913 | 3,333,846 | 0 | G | A | 46.5% | 27.0 / 115.3 | 86 | R46H (CGT→CAT) | ispB | all‑trans‑octaprenyl‑diphosphate synthase |
| * | NC_000913 | 1,911,754 | 0 | T | G | 45.7% | 47.2 / 14.8 | 35 | T275P (ACC→CCC) | htpX | zinc dependent endoprotease |
| * | NC_000913 | 4,098,155 | 0 | A | C | 41.4% | 161.8 / 43.6 | 111 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 1,978,427 | 0 | A | G | 40.8% | 27.5 / 88.6 | 71 | intergenic (‑230/+91) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| * | NC_000913 | 650,809 | 0 | T | G | 39.7% | 112.3 / 31.0 | 68 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 1,491,098 | 0 | A | C | 38.9% | 123.3 / 23.3 | 72 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 1,068,173 | 0 | T | G | 38.6% | 114.9 / 32.2 | 70 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 3,745,397 | 0 | A | C | 37.0% | 84.9 / 16.1 | 55 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 4,111,752 | 0 | T | C | 35.9% | 71.3 / 17.3 | 53 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 35.5% | 204.2 / 19.3 | 108 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 888,014 | 0 | T | G | 34.7% | 132.6 / 25.3 | 72 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,168,425 | 0 | T | G | 34.3% | 51.8 / 10.4 | 35 | noncoding (54/76 nt) | gltT | tRNA‑Glu |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 28 (0.290) | 16 (0.180) | 14/260 | 4.3 | 29.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 51 (0.560) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 31 (0.320) | 13 (0.140) | 13/260 | 4.6 | 24.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 52 (0.570) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 10 (0.110) | 7/262 | 6.6 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 4 (0.060) | 3/192 | 7.1 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 1411899 = | 76 (0.780) | 4 (0.050) | 4/226 | 7.3 | 6.3% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 58 (0.730) | pseudogene (51/51 nt) | ttcC | putative tRNA 2‑thiocytidine (s(2)C32) synthase | |||||