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 | 3,753,900 | 0 | A | G | 44.2% | 43.3 / 171.8 | 129 | V67A (GTC→GCC) | yiaV | putative membrane fusion protein |
| * | NC_000913 | 4,604,344 | 0 | C | T | 35.9% | 79.7 / 38.0 | 64 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 650,809 | 0 | T | G | 34.1% | 62.0 / 17.8 | 44 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 33.9% | 87.1 / 26.0 | 57 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,825,061 | 0 | G | A | 32.1% | 36.3 / 13.2 | 28 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.7% | 173.2 / 12.8 | 92 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 29.6% | 138.3 / 60.7 | 81 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 372,640 | 0 | T | G | 28.9% | 83.2 / 11.7 | 45 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 3,240,985 | 0 | T | G | 27.6% | 113.5 / 19.9 | 58 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.4% | 113.3 / 33.3 | 62 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 27.0% | 89.4 / 17.1 | 37 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,125 | 0 | T | A | 26.3% | 80.7 / 12.2 | 38 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 445,558 | 0 | A | C | 24.2% | 61.6 / 11.8 | 33 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,628,625 | 0 | A | C | 21.9% | 88.9 / 10.4 | 41 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 3,404,215 | 0 | T | G | 21.5% | 153.0 / 16.6 | 65 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,404,218 | 0 | T | G | 20.3% | 154.0 / 14.8 | 64 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,745,397 | 0 | A | C | 20.2% | 239.3 / 10.6 | 115 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 29,496 | 0 | T | A | 20.0% | 116.1 / 10.7 | 45 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,161,148 | 0 | G | A | 20.0% | 224.3 / 18.9 | 95 | E28K (GAA→AAA) | fabR | DNA‑binding transcriptional repressor FabR |
| * | NC_000913 | 4,568,512 | 0 | C | A | 20.0% | 206.7 / 20.6 | 75 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| 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 | 60 (0.700) | 20 (0.250) | 16/258 | 3.5 | 24.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 68 (0.850) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 11 (0.160) | 7/216 | 5.2 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 4542682 = | 61 (0.710) | 10 (0.120) | 8/258 | 5.7 | 13.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 69 (0.860) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 5 (0.070) | 4/216 | 6.6 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 6 (0.090) | 3/216 | 7.2 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 4 (0.060) | 3/224 | 7.3 | 5.9% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 64 (0.920) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 4475140 | 76 (0.920) | 5 (0.060) +TGGT |
3/258 | 8.0 | 6.1% | coding (279/453 nt) | tabA | DUF386 domain‑containing toxin‑antitoxin biofilm protein TabA |
| ? | NC_000913 | 4475141 = | 79 (0.920) | coding (280/453 nt) | tabA | DUF386 domain‑containing toxin‑antitoxin biofilm protein TabA | |||||
| * | ? | NC_000913 | 96424 = | 120 (1.400) | 4 (0.050) | 3/266 | 8.2 | 4.6% | coding (423/1083 nt) | mraY | phospho‑N‑acetylmuramoyl‑pentapeptide‑ transferase |
| ? | NC_000913 | = 1484094 | 49 (0.590) | coding (1034/3903 nt) | hrpA | ATP‑dependent RNA helicase HrpA | |||||
| * | ? | NC_000913 | = 3375829 | 86 (1.000) | 4 (0.050) | 3/276 | 8.3 | 4.9% | coding (961/1368 nt) | dcuD | putative transporter DcuD |
| ? | NC_000913 | = 3375883 | 69 (0.800) | coding (1015/1368 nt) | dcuD | putative transporter DcuD | |||||
| * | ? | NC_000913 | = 1053152 | 120 (1.400) | 3 (0.040) | 3/272 | 8.3 | 2.5% | coding (211/1074 nt) | yccM | putative 4Fe‑4S membrane protein |
| ? | NC_000913 | 1053156 = | 120 (1.420) | coding (207/1074 nt) | yccM | putative 4Fe‑4S membrane protein | |||||