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 31 shown, sorted by frequency from high to low) | |||||||||||
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seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
* | NC_000913 | 4,604,344 | 0 | C | T | 48.3% | 82.2 / 111.6 | 120 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
* | NC_000913 | 4,296,060 | 0 | C | T | 33.3% | 185.3 / 105.6 | 117 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
* | NC_000913 | 29,496 | 0 | T | A | 32.5% | 138.0 / 50.8 | 77 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
* | NC_000913 | 2,001,918 | 0 | A | C | 31.8% | 141.7 / 41.1 | 88 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
* | NC_000913 | 3,206,435 | 0 | C | T | 31.5% | 121.0 / 44.2 | 73 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
* | NC_000913 | 650,809 | 0 | T | G | 30.4% | 244.0 / 44.1 | 139 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
* | NC_000913 | 1,068,173 | 0 | T | G | 29.5% | 208.9 / 37.1 | 112 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
* | NC_000913 | 4,568,504 | 0 | T | G | 28.9% | 305.3 / 20.2 | 160 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
* | NC_000913 | 4,111,747 | 0 | G | T | 28.6% | 158.7 / 38.7 | 63 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
* | NC_000913 | 501,575 | 0 | A | C | 27.4% | 162.4 / 33.9 | 84 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
* | NC_000913 | 753,125 | 0 | T | A | 26.1% | 258.7 / 39.2 | 111 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
* | NC_000913 | 501,564 | 0 | A | C | 25.8% | 177.1 / 38.6 | 89 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
* | NC_000913 | 770,897 | 0 | T | G | 25.0% | 174.0 / 18.0 | 93 | intergenic (+286/‑561) | mngB/cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
* | NC_000913 | 2,326,450 | 0 | T | G | 25.0% | 157.1 / 37.9 | 80 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
* | NC_000913 | 3,943,488 | 0 | T | G | 25.0% | 129.9 / 11.4 | 68 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
* | NC_000913 | 3,206,444 | 0 | T | A | 23.9% | 157.3 / 26.1 | 71 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
* | NC_000913 | 3,240,985 | 0 | T | G | 23.6% | 261.5 / 35.8 | 123 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
* | NC_000913 | 3,404,215 | 0 | T | G | 23.6% | 224.6 / 37.0 | 106 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
* | NC_000913 | 646,747 | 0 | T | G | 23.5% | 242.8 / 58.8 | 119 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
* | NC_000913 | 888,014 | 0 | T | G | 23.1% | 202.7 / 15.4 | 91 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | = 4542690 | 149 (1.010) | 22 (0.160) | 17/258 | 5.6 | 14.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
? | NC_000913 | = 4542986 | 131 (0.950) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
* | ? | NC_000913 | = 375219 | NA (NA) | 9 (0.080) | 9/216 | 7.1 | NA | noncoding (1/36 nt) | other | REP31f |
? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | 374921 = | NA (NA) | 15 (0.150) | 7/190 | 7.2 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | = 375118 | NA (NA) | 8 (0.070) | 8/216 | 7.5 | NA | noncoding (1/36 nt) | other | REP31d |
? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | = 375320 | NA (NA) | 8 (0.060) | 8/232 | 7.9 | NA | noncoding (1/36 nt) | other | REP31h |
? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | = 374958 | NA (NA) | 6 (0.060) | 6/202 | 8.0 | NA | noncoding (28/34 nt) | other | REP31a |
? | NC_000913 | = 377392 | NA (NA) | noncoding (31/34 nt) | other | REP32b | |||||
* | ? | NC_000913 | 4542682 = | 166 (1.120) | 9 (0.070) | 9/258 | 8.1 | 5.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
? | NC_000913 | 4542996 = | 133 (0.960) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
* | ? | NC_000913 | 375023 = | NA (NA) | 12 (0.120) | 5/192 | 8.2 | NA | intergenic (+142/‑436) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
* | ? | NC_000913 | 375248 = | NA (NA) | 13 (0.100) | 6/238 | 9.0 | NA | noncoding (15/34 nt) | other | REP31g |
? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
* | ? | NC_000913 | 374922 = | NA (NA) | 19 (0.140) | 6/260 | 9.5 | 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 |