mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 43.0% | 109.5 / 89.0 | 128 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 29.4% | 164.0 / 30.7 | 85 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.9% | 250.0 / 20.0 | 135 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 28.8% | 121.2 / 27.5 | 66 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.7% | 240.4 / 41.8 | 90 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 29,496 | 0 | T | A | 25.7% | 169.3 / 23.4 | 74 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 25.7% | 165.5 / 18.6 | 74 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 25.7% | 209.5 / 28.5 | 113 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,429,984 | 0 | T | G | 24.6% | 265.3 / 39.2 | 118 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.8% | 341.3 / 102.5 | 172 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 650,809 | 0 | T | G | 23.7% | 215.8 / 18.1 | 97 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 23.5% | 114.7 / 13.4 | 51 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,111,752 | 0 | T | C | 22.9% | 206.2 / 15.5 | 96 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 646,747 | 0 | T | G | 22.4% | 159.2 / 22.0 | 67 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 22.2% | 316.8 / 31.8 | 135 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,404,218 | 0 | T | G | 22.0% | 302.8 / 38.7 | 132 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 21.8% | 409.0 / 22.2 | 174 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 3,556,205 | 0 | A | C | 21.8% | 195.3 / 12.5 | 78 | S215R (AGT→AGG) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,679,688 | 0 | T | G | 21.6% | 210.9 / 17.1 | 88 | G44G (GGT→GGG) | ydgI | putative arginine:ornithine antiporter |
| * | NC_000913 | 3,240,985 | 0 | T | G | 20.9% | 260.6 / 26.1 | 110 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 13 (0.100) | 13/278 | 6.7 | 100% | intergenic (‑56/‑482) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101745 = | NA (NA) | intergenic (‑1/+150) | wbbL/insH‑7 | interrupted rhamnosyltransferase WbbL/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 4542682 = | 115 (0.860) | 11 (0.090) | 10/260 | 7.3 | 8.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 121 (0.970) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4349388 | 130 (0.970) | 13 (0.100) | 11/278 | 7.4 | 9.1% | coding (647/720 nt) | dcuR | DNA‑binding transcriptional activator DcuR |
| ? | NC_000913 | 4349399 = | 129 (0.970) | coding (636/720 nt) | dcuR | DNA‑binding transcriptional activator DcuR | |||||
| * | ? | NC_000913 | = 4542690 | 105 (0.790) | 9 (0.070) | 8/260 | 8.1 | 7.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 121 (0.970) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1978494 | 0 (0.000) | 21 (0.160) | 8/278 | 8.5 | 100% | intergenic (‑297/+24) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 6 (0.060) | 5/226 | 8.7 | 4.7% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 122 (1.130) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 3137211 = | 140 (1.050) | 6 (0.050) | 5/264 | 9.7 | 4.0% | coding (1312/1860 nt) | gss | fused glutathionylspermidine amidase/glutathionylspermidine synthetase |
| ? | NC_000913 | 3137337 = | 155 (1.220) | coding (1186/1860 nt) | gss | fused glutathionylspermidine amidase/glutathionylspermidine synthetase | |||||
| * | ? | NC_000913 | = 2129475 | 143 (1.070) | 8 (0.060) | 5/270 | 9.8 | 5.2% | coding (176/747 nt) | wcaE | putative colanic acid biosynthesis glycosyl transferase |
| ? | NC_000913 | = 2129564 | 155 (1.200) | coding (87/747 nt) | wcaE | putative colanic acid biosynthesis glycosyl transferase | |||||
| * | ? | NC_000913 | 1780767 = | 126 (0.940) | 6 (0.050) | 4/260 | 10.1 | 5.0% | coding (367/939 nt) | ydiR | putative electron transfer flavoprotein subunit YdiR |
| ? | NC_000913 | 1780852 = | 110 (0.880) | coding (452/939 nt) | ydiR | putative electron transfer flavoprotein subunit YdiR | |||||
| * | ? | NC_000913 | 2683552 = | 171 (1.280) | 6 (0.050) | 4/266 | 10.3 | 3.8% | coding (690/1194 nt) | yphH | putative DNA‑binding transcriptional regulator, NAGC‑like |
| ? | NC_000913 | 2683644 = | 141 (1.100) | coding (782/1194 nt) | yphH | putative DNA‑binding transcriptional regulator, NAGC‑like | |||||