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 25 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 39.4% | 108.9 / 73.4 | 104 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,943,488 | 0 | T | G | 37.1% | 29.8 / 12.4 | 35 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 753,125 | 0 | T | A | 33.0% | 217.4 / 54.5 | 115 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 30.4% | 88.2 / 17.2 | 46 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.8% | 260.3 / 25.8 | 138 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,556,207 | 0 | T | C | 29.8% | 78.5 / 15.7 | 47 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,209,827 | 0 | T | G | 27.5% | 61.9 / 13.3 | 40 | noncoding (54/76 nt) | gltV | tRNA‑Glu |
| * | NC_000913 | 2,001,918 | 0 | A | C | 27.4% | 199.6 / 39.6 | 95 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,825,061 | 0 | G | A | 27.0% | 71.8 / 11.0 | 37 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.7% | 148.1 / 44.8 | 74 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.4% | 276.4 / 88.8 | 138 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 445,558 | 0 | A | C | 25.0% | 91.8 / 14.8 | 44 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.0% | 190.8 / 29.3 | 84 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 1,775,467 | 0 | A | C | 24.5% | 215.7 / 13.8 | 94 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 24.0% | 211.6 / 28.5 | 75 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 646,747 | 0 | T | G | 23.7% | 169.7 / 33.6 | 76 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 650,809 | 0 | T | G | 23.6% | 164.3 / 15.4 | 72 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 372,640 | 0 | T | G | 23.6% | 210.5 / 24.1 | 89 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 29,496 | 0 | T | A | 23.5% | 187.7 / 31.0 | 81 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,531,440 | 0 | A | C | 20.9% | 264.3 / 20.8 | 106 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 125 (1.020) | 28 (0.240) | 24/258 | 3.4 | 19.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 120 (1.050) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 118 (0.960) | 15 (0.130) | 13/258 | 6.0 | 11.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 121 (1.060) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 5 (0.060) | 5/190 | 7.4 | 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 | 374922 = | NA (NA) | 11 (0.100) | 5/260 | 9.3 | 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 | 1979486 = | 164 (1.340) | 30 (0.240) | 5/276 | 9.7 | 15.5% | intergenic (‑271/‑267) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 340035 = | NA (NA) | 7 (0.060) | 5/274 | 9.7 | NA | coding (243/297 nt) | yahH | putative uncharacterized protein YahH |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1979633 | 160 (1.310) | 22 (0.180) | 4/276 | 10.3 | 12.1% | intergenic (‑418/‑120) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 523265 | 83 (0.680) | 6 (0.050) | 4/276 | 10.3 | 7.9% | coding (5/4281 nt) | rhsD | protein RhsD |
| ? | NC_000913 | = 523314 | 57 (0.470) | coding (54/4281 nt) | rhsD | protein RhsD | |||||
| * | ? | NC_000913 | 1462089 = | 106 (0.860) | 4 (0.040) | 3/252 | 10.4 | 3.0% | coding (1197/1206 nt) | paaJ | beta‑ketoadipyl‑CoA thiolase |
| ? | NC_000913 | 1462223 = | 164 (1.470) | coding (99/1314 nt) | paaK | phenylacetate‑CoA ligase | |||||
| * | ? | NC_000913 | = 4373296 | NA (NA) | 3 (0.030) | 3/256 | 10.5 | NA | noncoding (1/34 nt) | other | REP328b |
| ? | NC_000913 | = 4374496 | NA (NA) | intergenic (‑262/+133) | yjeJ/epmB | protein YjeJ/lysine 2,3‑aminomutase | |||||