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 |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 123,466 | T→G | 40.3% | A150A (GCT→GCG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 238,497 | G→T | 25.3% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 27.0% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,507 | G→T | 21.9% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 27.9% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 26.9% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 298,557 | A→C | 37.9% | L57R (CTC→CGC) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 454,873 | C→G | 53.0% | intergenic (+84/‑260) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,877 | A→T | 28.5% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,885 | C→G | 37.7% | intergenic (+96/‑248) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 488,808 | C→G | 24.5% | A758G (GCG→GGG) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 713,903 | Δ1 bp | 7.3% | coding (346/1641 nt) | pgm → | phosphoglucomutase |
| RA | 747,550 | G→A | 9.7% | L74F (CTC→TTC) | abrB ← | putative regulator |
| RA | 781,548 | G→T | 10.9% | intergenic (+104/‑29) | lysZ → / → lysQ | tRNA‑Lys/tRNA‑Lys |
| RA | 835,277 | C→T | 10.2% | I10I (ATC→ATT) | ybiB → | nonspecific DNA‑binding protein YbiB |
| RA | 904,995 | G→A | 10.8% | G28E (GGA→GAA) | amiD → | N‑acetylmuramoyl‑L‑alanine amidase D |
| MC JC | 932,613 | Δ459 bp | 100% | coding (19‑477/495 nt) | lrp → | DNA‑binding transcriptional dual regulator Lrp |
| RA | 983,817 | T→A | 6.3% | H56Q (CAT→CAA) | gloC → | hydroxyacylglutathione hydrolase GloC |
| RA | 1,233,571 | C→T | 9.6% | A383T (GCA→ACA) | nhaB ← | Na(+):H(+) antiporter NhaB |
| RA | 1,249,880 | C→T | 11.3% | C320Y (TGC→TAC) | dhaK ← | dihydroxyacetone kinase subunit K |
| RA | 1,738,542 | C→T | 11.4% | I233I (ATC→ATT) | purR → | DNA‑binding transcriptional repressor PurR |
| RA | 1,755,562 | C→A | 9.9% | intergenic (‑421/‑136) | fumD ← / → pykF | fumarase D/pyruvate kinase I |
| RA | 1,767,304 | A→G | 9.7% | L461S (TTG→TCG) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,850,096 | C→T | 8.0% | Y420Y (TAC→TAT) | sppA → | protease IV, a signal peptide peptidase |
| RA | 1,913,867 | Δ1 bp | 8.3% | coding (950/2049 nt) | prc ← | tail‑specific protease |
| RA | 1,913,868 | Δ1 bp | 8.3% | coding (949/2049 nt) | prc ← | tail‑specific protease |
| RA | 1,924,759 | C→T | 9.1% | E71K (GAA→AAA) | yobA ← | CopC domain‑containing protein |
| RA | 1,937,378 | C→T | 10.8% | Q243* (CAG→TAG) | yebK → | DNA‑binding transcriptional repressor YebK |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,245 | G→T | 49.8% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,230,809 | G→A | 12.1% | P62P (CCG→CCA) | yohJ → | PF03788 family membrane protein YohJ |
| RA | 2,255,233 | G→T | 27.9% | intergenic (‑47/‑122) | rihB ← / → yeiL | pyrimidine‑specific ribonucleoside hydrolase RihB/putative DNA‑binding transcriptional regulator YeiL |
| RA | 2,314,181 | G→T | 23.2% | D232Y (GAT→TAT) | rcsD → | RcsD phosphotransferase |
| RA | 2,523,679 | C→T | 9.1% | A103T (GCG→ACG) | xapB ← | xanthosine:H(+) symporter XapB |
| RA | 2,700,031 | A→G | 8.5% | intergenic (+108/+86) | yfhL → / ← shoB | putative 4Fe‑4S cluster‑containing protein YfhL/toxic peptide ShoB |
| RA | 2,741,347 | A→T | 9.7% | intergenic (‑197/‑13) | aroF ← / → yfiL | 3‑deoxy‑7‑phosphoheptulonate synthase, Tyr‑sensitive/DUF2799 domain‑containing lipoprotein YfiL |
| RA | 2,955,849 | C→T | 7.0% | R52H (CGC→CAC) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,964,722 | G→T | 7.4% | P145Q (CCG→CAG) | thyA ← | thymidylate synthase |
| RA | 3,133,652 | G→A | 6.0% | C102C (TGC→TGT) | yghS ← | putative ATP‑binding protein YghS |
| RA | 3,140,205 | G→C | 30.6% | C38W (TGC→TGG) | hybF ← | hydrogenase maturation protein HybF |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,578,889 | A→C | 18.0% | intergenic (‑163/+61) | gntR ← / ← yhhW | DNA‑binding transcriptional repressor GntR/quercetin 2,3‑dioxygenase |
| RA | 3,655,801 | T→A | 5.9% | T34T (ACA→ACT) | yhiD ← | inner membrane protein YhiD |
| RA | 3,828,980 | A→C | 50.0% | Q12H (CAA→CAC) | xanP → | xanthine:H(+) symporter XanP |
| RA | 4,102,252 | A→T | 8.7% | D188V (GAC→GTC) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| RA | 4,106,264 | T→A | 7.7% | W149R (TGG→AGG) | cpxP → | periplasmic protein CpxP |
| RA | 4,183,097 | A→T | 100% | Q618L (CAG→CTG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 33.8% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,332,190 | G→T | 8.5% | W25C (TGG→TGT) N361K (AAC→AAA) |
pmrR → basS ← |
putative bitopic inner membrane protein sensory histidine kinase BasS |
| RA | 4,333,535 | C→A | 14.3% | R139L (CGT→CTT) | basR ← | DNA‑binding transcriptional dual regulator BasR |
| RA | 4,373,626 | T→C | 9.7% | K203K (AAA→AAG) | yjeJ ← | protein YjeJ |
| RA | 4,460,012 | T→C | 8.0% | Q118R (CAG→CGG) | nrdG ← | anaerobic ribonucleoside‑triphosphate reductase activating protein |
| RA | 4,602,615 | C→A | 8.6% | V82L (GTG→TTG) | yjjP ← | putative succinate exporter YjjP |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423747–3424233 | 3424530–3424238 | 6–784 | 10 [9] | [9] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 32 (0.740) | 20 (0.540) | 15/204 | NT | 44.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 22 (0.590) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 29 (0.670) | 8 (0.220) | 7/204 | NT | 25.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 22 (0.590) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 35 (0.840) | 29/228 | NT | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 2999468 = | 41 (0.950) | 25 (0.590) | 22/234 | NT | 37.1% | coding (424/756 nt) | ygeR | LysM domain‑containing putative peptidase lipoprotein YgeR |
| ? | NC_000913 | = 3819586 | 44 (1.030) | coding (1585/1683 nt) | ligB | DNA ligase B | |||||