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 | 45.5% | 61.4 / 71.7 | 88 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 36.8% | 52.1 / 51.4 | 57 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 29,496 | 0 | T | A | 36.5% | 77.8 / 35.8 | 52 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,296,060 | 0 | C | T | 32.7% | 160.9 / 94.0 | 107 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.9% | 59.6 / 15.2 | 39 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 27.3% | 55.9 / 14.1 | 33 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.3% | 163.6 / 13.3 | 88 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 650,809 | 0 | T | G | 26.6% | 142.7 / 26.7 | 79 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 25.7% | 64.9 / 13.2 | 35 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,404,215 | 0 | T | G | 25.3% | 159.0 / 29.5 | 83 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 372,640 | 0 | T | G | 24.1% | 103.1 / 11.1 | 54 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 786,855 | 0 | A | C | 23.5% | 105.8 / 11.8 | 51 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 23.5% | 237.4 / 21.1 | 115 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 3,401,459 | 0 | T | C | 23.5% | 172.6 / 19.8 | 81 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 366,526 | 0 | T | G | 22.2% | 110.7 / 18.7 | 54 | T329P (ACC→CCC) | lacI | DNA‑binding transcriptional repressor LacI |
| * | NC_000913 | 175,694 | 0 | T | G | 21.6% | 154.9 / 17.6 | 74 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 4,111,747 | 0 | G | T | 21.6% | 110.6 / 14.4 | 37 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,098,155 | 0 | A | C | 20.9% | 209.8 / 20.0 | 105 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 646,747 | 0 | T | G | 20.0% | 99.2 / 11.2 | 45 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| 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 | 4542682 = | 76 (0.800) | 13 (0.150) | 10/258 | 5.0 | 13.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 92 (1.030) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1979340 | 47 (0.490) | 16 (0.170) | 7/276 | 6.3 | 25.4% | intergenic (‑125/‑413) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1979337 = | 44 (0.460) | 9 (0.090) | 6/276 | 6.7 | 17.0% | intergenic (‑122/‑416) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102943 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1396044 = | NA (NA) | 5 (0.050) | 5/276 | 7.2 | 6.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1979421 | 69 (0.720) | intergenic (‑206/‑332) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 1979337 = | 44 (0.460) | 7 (0.080) | 4/268 | 7.5 | 14.1% | intergenic (‑122/‑416) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2067353 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 4452877 | 83 (0.870) | 4 (0.040) | 4/274 | 7.6 | 4.6% | coding (307/1026 nt) | ytfT | galactofuranose ABC transporter putative membrane subunit YtfT |
| ? | NC_000913 | 4452881 = | 84 (0.890) | coding (311/1026 nt) | ytfT | galactofuranose ABC transporter putative membrane subunit YtfT | |||||
| * | ? | NC_000913 | = 526706 | 81 (0.850) | 5 (0.050) | 4/274 | 7.6 | 5.8% | coding (3446/4281 nt) | rhsD | protein RhsD |
| ? | NC_000913 | 526710 = | 81 (0.850) | coding (3450/4281 nt) | rhsD | protein RhsD | |||||
| * | ? | NC_000913 | 2657858 = | 105 (1.100) | 3 (0.030) | 3/262 | 8.0 | 3.1% | coding (1078/1851 nt) | hscA | iron‑sulfur cluster biosynthesis chaperone HscA |
| ? | NC_000913 | 2657948 = | 86 (0.950) | coding (988/1851 nt) | hscA | iron‑sulfur cluster biosynthesis chaperone HscA | |||||