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 32 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,209,827 | 0 | T | G | 38.5% | 51.0 / 11.2 | 39 | noncoding (54/76 nt) | gltV | tRNA‑Glu |
| * | NC_000913 | 3,556,205 | 0 | A | C | 36.6% | 72.2 / 15.8 | 41 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,906,769 | 0 | A | C | 34.6% | 87.3 / 13.9 | 52 | Y98D (TAT→GAT) | rlmA | 23S rRNA m(1)G745 methyltransferase |
| * | NC_000913 | 3,745,397 | 0 | A | C | 33.9% | 111.6 / 13.7 | 66 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 3,556,207 | 0 | T | C | 33.3% | 61.0 / 15.4 | 42 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,943,488 | 0 | T | G | 33.3% | 49.0 / 12.6 | 36 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 372,640 | 0 | T | G | 32.8% | 124.8 / 20.1 | 61 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 31.9% | 106.1 / 34.1 | 72 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,740,909 | 0 | T | G | 31.1% | 154.9 / 19.4 | 74 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.9% | 200.4 / 15.5 | 95 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 650,809 | 0 | T | G | 30.2% | 110.6 / 14.5 | 53 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.6% | 142.0 / 21.3 | 63 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,032,731 | 0 | T | G | 28.4% | 141.3 / 20.3 | 67 | G80G (GGT→GGG) | yigZ | IMPACT family member YigZ |
| * | NC_000913 | 2,667,126 | 0 | A | C | 28.3% | 199.7 / 27.8 | 92 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 388,336 | 0 | A | C | 28.2% | 153.9 / 10.3 | 72 | N181T (AAC→ACC) | tauD | taurine dioxygenase |
| * | NC_000913 | 1,550,663 | 0 | A | C | 27.9% | 97.2 / 13.5 | 43 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 3,619,268 | 0 | T | G | 27.3% | 148.1 / 11.5 | 66 | V26G (GTA→GGA) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 2,782,509 | 0 | A | C | 26.3% | 263.3 / 24.1 | 114 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 3,844,219 | 0 | T | G | 26.1% | 220.5 / 19.2 | 92 | F86V (TTT→GTT) | adeD | adenine deaminase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.0% | 71.8 / 13.9 | 36 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| 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 | = 1207805 | 66 (0.740) | 17 (0.220) | 16/246 | 3.2 | 24.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 45 (0.570) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 31 (0.350) | 15 (0.180) | 14/260 | 3.9 | 27.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 50 (0.600) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 34 (0.380) | 13 (0.160) | 13/260 | 4.1 | 24.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 49 (0.590) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 14 (0.160) | 10/278 | 5.3 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 8 (0.130) | 5/192 | 5.5 | 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 | 1979271 = | 0 (0.000) | 10 (0.110) | 8/278 | 6.0 | 100% | intergenic (‑56/‑482) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 4373261 = | NA (NA) | 13 (0.180) | 5/228 | 6.3 | NA | intergenic (+99/+104) | yjeI/yjeJ | DUF4156 domain‑containing lipoprotein YjeI/protein YjeJ |
| ? | NC_000913 | 4374533 = | NA (NA) | intergenic (‑299/+96) | yjeJ/epmB | protein YjeJ/lysine 2,3‑aminomutase | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 4 (0.070) | 3/192 | 6.6 | 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 | = 1428500 | 98 (1.110) | 4 (0.050) +CGC |
3/270 | 8.2 | 4.0% | noncoding (295/1196 nt) | IS5 | repeat region |
| ? | NC_000913 | 2067066 = | NA (NA) | noncoding (288/1195 nt) | IS5 | repeat region | |||||