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 | 4,604,344 | 0 | C | T | 39.7% | 81.9 / 47.4 | 73 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 35.4% | 60.4 / 32.9 | 48 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 31.7% | 90.5 / 25.6 | 41 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,444 | 0 | T | A | 28.0% | 94.0 / 15.7 | 50 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.7% | 236.4 / 18.2 | 120 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,491,103 | 0 | A | C | 26.7% | 116.4 / 12.9 | 60 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 753,125 | 0 | T | A | 26.3% | 115.1 / 19.9 | 57 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.3% | 181.1 / 59.9 | 95 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,401,459 | 0 | T | C | 25.0% | 126.7 / 13.7 | 68 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 1,068,173 | 0 | T | G | 24.6% | 165.7 / 11.6 | 69 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 753,114 | 0 | G | T | 24.6% | 146.7 / 10.7 | 57 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,435,727 | 0 | G | A | 23.1% | 82.4 / 12.1 | 39 | intergenic (‑108/+33) | uspF/ompN | nucleotide binding filament protein/outer membrane porin N |
| * | NC_000913 | 29,496 | 0 | T | A | 22.7% | 98.8 / 13.8 | 44 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 22.7% | 156.4 / 16.9 | 66 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 802,118 | 0 | A | C | 22.6% | 124.9 / 10.5 | 55 | T78P (ACC→CCC) | ybhI | putative tricarboxylate transporter |
| * | NC_000913 | 4,098,155 | 0 | A | C | 22.5% | 207.7 / 14.4 | 90 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 1,491,098 | 0 | A | C | 22.2% | 140.6 / 10.3 | 63 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 332,991 | 0 | G | T | 21.5% | 218.1 / 22.5 | 79 | L207F (TTG→TTT) | pdeL | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 731,392 | 0 | A | G | 20.3% | 153.7 / 32.1 | 69 | T604A (ACC→GCC) | rhsC | rhs element protein RhsC |
| 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 | = 374963 | NA (NA) | 9 (0.170) | 6/192 | 4.7 | 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 | = 1207805 | 52 (0.660) | 8 (0.120) | 7/246 | 5.3 | 14.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 48 (0.690) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 2406540 | 87 (1.270) | 10 (0.140) +GCGGCAGCT |
5/226 | 5.8 | 9.2% | coding (102/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA |
| ? | NC_000913 | 2406541 = | 113 (1.440) | coding (101/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA | |||||
| * | ? | NC_000913 | = 2776238 | 100 (1.280) | 3 (0.040) | 3/264 | 7.6 | 3.3% | coding (320/459 nt) | yfjX | CP4‑57 prophage; putative antirestriction protein |
| ? | NC_000913 | = 2776316 | 79 (1.060) | coding (398/459 nt) | yfjX | CP4‑57 prophage; putative antirestriction protein | |||||
| * | ? | NC_000913 | = 2743877 | 78 (1.000) | 3 (0.040) | 3/272 | 7.7 | 4.0% | coding (253/483 nt) | yfiB | lipoprotein YfiB |
| ? | NC_000913 | = 2743957 | 69 (0.900) | coding (333/483 nt) | yfiB | lipoprotein YfiB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 3 (0.040) | 3/270 | 7.7 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377387 | NA (NA) | intergenic (+76/+148) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 3777889 = | 65 (0.830) | 3 (0.040) | 3/274 | 7.8 | 3.8% | coding (491/1656 nt) | lldP | lactate/glycolate:H(+) symporter LldP |
| ? | NC_000913 | 3778056 = | 87 (1.130) | coding (658/1656 nt) | lldP | lactate/glycolate:H(+) symporter LldP | |||||
| * | ? | NC_000913 | = 1979489 | 105 (1.340) | 5 (0.060) | 3/278 | 7.8 | 4.5% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||