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 24 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,852,717 | 0 | T | C | 62.5% | 352.3 / inf | 355 | V421V (GTA→GTG) | ydjE | putative transporter YdjE |
| * | NC_000913 | 32,997 | 0 | C | T | 61.7% | 288.1 / inf | 274 | I727I (ATC→ATT) | carB | carbamoyl phosphate synthetase subunit beta |
| * | NC_000913 | 3,105,790 | 0 | G | A | 60.5% | 263.2 / inf | 301 | G26D (GGC→GAC) | nupG | nucleoside:H(+) symporter NupG |
| * | NC_000913 | 3,577,599 | 1 | . | C | 58.5% | 685.5 / inf | 296 | intergenic (‑7/+132) | gntK/gntR | D‑gluconate kinase, thermostable/DNA‑binding transcriptional repressor GntR |
| * | NC_000913 | 1,671,369 | 0 | T | C | 55.8% | 136.6 / inf | 276 | intergenic (+417/‑7) | ynfM/asr | putative transporter YnfM/acid shock protein |
| * | NC_000913 | 1,004,153 | 2 | . | G | 51.1% | 268.7 / 301.3 | 131 | coding (207/711 nt) | ycbF | putative fimbrial chaperone YcbF |
| * | NC_000913 | 3,072,455 | 0 | T | C | 49.5% | 50.0 / inf | 315 | V56V (GTA→GTG) | pgk | phosphoglycerate kinase |
| * | NC_000913 | 98,205 | 0 | C | T | 37.3% | 329.7 / inf | 330 | D373D (GAC→GAT) | murD | UDP‑N‑acetylmuramoyl‑L‑alanine‑‑D‑glutamate ligase |
| * | NC_000913 | 482,473 | 0 | A | G | 35.4% | 389.7 / inf | 311 | V644A (GTT→GCT) | acrB | multidrug efflux pump RND permease AcrB |
| * | NC_000913 | 4,296,041 | 0 | A | G | 34.6% | 783.9 / inf | 562 | intergenic (+247/+395) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.7% | 1062.2 / inf | 561 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,043,284 | 0 | A | G | 26.7% | 854.8 / inf | 412 | intergenic (‑136/+28) | yqfA/yqfB | hemolysin‑III family protein/PUA‑like domain‑containing protein YqfB |
| * | NC_000913 | 2,159,950 | 0 | T | C | 26.3% | 537.0 / 231.5 | 279 | V522A (GTG→GCG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 2,017,664 | 0 | T | C | 26.0% | 637.2 / 255.7 | 315 | S371P (TCG→CCG) | fliI | flagellum‑specific ATP synthase FliI |
| * | NC_000913 | 3,555,607 | 0 | G | A | 25.7% | 689.9 / 292.3 | 343 | W841* (TGG→TGA) | malT | DNA‑binding transcriptional activator MalT |
| * | NC_000913 | 2,745,605 | 0 | T | C | 25.7% | 462.2 / 184.0 | 230 | D105G (GAC→GGC) | rimM | ribosome maturation factor RimM |
| * | NC_000913 | 2,008,878 | 0 | T | C | 24.7% | 586.0 / 215.6 | 283 | M201T (ATG→ACG) | yedE | putative selenium transporter YedE |
| * | NC_000913 | 3,014,864 | 0 | G | A | 24.2% | 615.2 / 231.8 | 301 | P65L (CCC→CTC) | yqeC | uncharacterized protein YqeC |
| * | NC_000913 | 1,851,664 | 0 | A | G | 23.6% | 650.1 / 210.4 | 288 | N269D (AAC→GAC) | ansA | L‑asparaginase 1 |
| * | NC_000913 | 4,232,715 | 0 | A | G | 22.7% | 751.5 / 224.4 | 326 | R173R (CGT→CGC) | lysC | aspartate kinase III |
| 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 | 1207790 = | 236 (0.710) | 140 (0.500) | 88/162 | 4.6 | 43.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 174 (0.630) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 256 (0.770) | 84 (0.300) | 63/162 | 9.9 | 30.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 161 (0.580) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 71350 | 369 (1.110) | 145 (0.450) | 58/188 | 14.1 | 44.8% | intergenic (+85/‑1) | araC/yabI | DNA‑binding transcriptional dual regulator AraC/DedA family protein YabI |
| ? | NC_000913 | = 2857042 | 0 (0.000) | intergenic (‑236/‑51) | ygbA/mutS | protein YgbA/DNA mismatch repair protein MutS | |||||
| * | ? | NC_000913 | = 4542690 | 407 (1.220) | 20 (0.070) | 18/176 | 28.3 | 5.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 396 (1.310) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1209618 | 215 (0.650) | 18 (0.060) | 14/164 | 29.3 | 6.7% | pseudogene (38/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment |
| ? | NC_000913 | 2471897 = | 321 (1.140) | pseudogene (166/519 nt) | yfdL | CPS‑53 (KpLE1) prophage; putative uncharacterized protein YfdL | |||||
| * | ? | NC_000913 | 4542682 = | 418 (1.250) | 17 (0.060) | 16/176 | 29.4 | 4.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 397 (1.310) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||