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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 805,885 | 0 | C | T | 68.4% | 26.6 / 12.2 | 19 | intergenic (+121/+113) | ybhJ/ybhC | putative hydratase YbhJ/outer membrane lipoprotein YhbC |
| * | NC_000913 | 4,628,643 | 1 | . | A | 66.7% | 86.8 / 39.8 | 39 | intergenic (+96/+212) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 734,682 | 0 | A | G | 53.3% | ‑0.8 / 31.4 | 31 | pseudogene (463/1434 nt) | ybfO | conserved protein, rhs‑like YbfO |
| * | NC_000913 | 3,390,722 | 0 | T | C | 52.2% | 5.1 / 60.7 | 46 | Q436R (CAG→CGG) | tldD | metalloprotease TldD |
| * | NC_000913 | 266,320 | 0 | G | A | 51.6% | 4.2 / 83.5 | 64 | G78G (GGC→GGT) | yafY | CP4‑6 prophage; inner membrane lipoprotein YafY |
| * | NC_000913 | 266,335 | 0 | G | A | 46.7% | 25.5 / 55.0 | 46 | R73R (CGC→CGT) | yafY | CP4‑6 prophage; inner membrane lipoprotein YafY |
| * | NC_000913 | 266,334 | 0 | G | C | 45.6% | 34.1 / 73.4 | 46 | Q74E (CAG→GAG) | yafY | CP4‑6 prophage; inner membrane lipoprotein YafY |
| * | NC_000913 | 266,347 | 0 | A | G | 42.3% | 19.2 / 28.0 | 26 | V69V (GTT→GTC) | yafY | CP4‑6 prophage; inner membrane lipoprotein YafY |
| * | NC_000913 | 4,296,060 | 0 | C | T | 35.3% | 41.2 / 28.0 | 34 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 266,355 | 0 | A | G | 34.8% | 32.1 / 16.4 | 23 | L67L (TTG→CTG) | yafY | CP4‑6 prophage; inner membrane lipoprotein YafY |
| * | NC_000913 | 733,011 | 0 | T | C | 32.0% | 63.4 / 38.9 | 51 | I1143I (ATT→ATC) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 732,990 | 0 | A | G | 29.8% | 64.4 / 34.3 | 48 | V1136V (GTA→GTG) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 3,765,557 | 0 | C | G | 29.2% | 47.8 / 17.2 | 25 | T1125T (ACC→ACG) | rhsA | rhs element protein RhsA |
| * | NC_000913 | 4,628,649 | 1 | . | C | 25.6% | 84.0 / 39.0 | 43 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 266,143 | 0 | T | C | 22.7% | 89.6 / 22.6 | 44 | L137L (CTA→CTG) | yafY | CP4‑6 prophage; inner membrane lipoprotein YafY |
| * | NC_000913 | 266,147 | 0 | T | C | 22.7% | 85.9 / 22.4 | 44 | Q136R (CAG→CGG) | yafY | CP4‑6 prophage; inner membrane lipoprotein YafY |
| * | NC_000913 | 732,974 | 0 | G | A | 21.9% | 80.2 / 14.6 | 41 | S1131N (AGC→AAC) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 266,149 | 0 | C | T | 21.7% | 98.8 / 21.7 | 46 | G135G (GGG→GGA) | yafY | CP4‑6 prophage; inner membrane lipoprotein YafY |
| 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 | = 4542690 | 32 (0.730) | 6 (0.150) | 5/258 | 3.1 | 12.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 56 (1.370) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 15386 | 12 (0.340) | 5 (0.140) | 4/224 | 3.1 | 29.4% | intergenic (+88/‑59) | dnaJ/insL‑1 | chaperone protein DnaJ/IS186/IS421 transposase |
| ? | NC_000913 | = 16731 | NA (NA) | noncoding (1345/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 7 (0.170) | 4/260 | 3.4 | 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 | = 3802195 | 68 (1.550) | 3 (0.070) | 3/272 | 3.9 | 4.3% | coding (864/1020 nt) | waaO | UDP‑D‑glucose:(glucosyl)LPS alpha‑1,3‑glucosyltransferase |
| ? | NC_000913 | 3802199 = | 68 (1.580) | coding (860/1020 nt) | waaO | UDP‑D‑glucose:(glucosyl)LPS alpha‑1,3‑glucosyltransferase | |||||
| * | ? | NC_000913 | = 2471293 | 59 (1.350) | 3 (0.070) | 3/270 | 3.9 | 5.0% | coding (225/441 nt) | yfdK | CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| ? | NC_000913 | 2471297 = | 57 (1.330) | coding (221/441 nt) | yfdK | CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK | |||||
| * | ? | NC_000913 | 340035 = | NA (NA) | 3 (0.070) | 3/274 | 4.0 | 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 | |||||