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 | 87,023 | A→G | 5.6% | E465G (GAG→GGG) | ilvI → | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| RA | 90,720 | C→A | 7.8% | R209R (CGC→CGA) | rsmH → | 16S rRNA m(4)C1402 methyltransferase |
| RA | 131,353 | A→G | 5.2% | intergenic (‑93/‑262) | yacH ← / → acnB | DUF3300 domain‑containing protein YacH/hypothetical protein |
| RA | 175,410 | C→A | 5.5% | P102T (CCG→ACG) | clcA → | chloride:H(+) antiporter ClcA |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 275,607 | G→A | 6.8% | V95M (GTG→ATG) | mmuP → | S‑methyl‑L‑methionine transporter |
| RA | 433,518 | C→A | 6.0% | H22N (CAT→AAT) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| RA | 515,859 | C→G | 100% | intergenic (‑86/‑60) | qmcA ← / → fetA | PHB domain‑containing protein/putative iron ABC exporter ATP‑binding subunit FetA |
| RA | 998,954 | T→C | 6.8% | A155A (GCT→GCC) | elfD → | putative fimbrial chaperone ElfD |
| RA | 1,547,239 | T→A | 6.3% | intergenic (‑70/‑162) | yddG ← / → fdnG | aromatic amino acid exporter/formate dehydrogenase N subunit alpha |
| RA | 1,688,337 | A→G | 5.1% | L14P (CTC→CCC) | fumA ← | fumarase A |
| RA | 1,767,640 | T→C | 5.6% | N349S (AAC→AGC) | ydiJ ← | putative FAD‑linked oxidoreductase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,011,665 | G→T | 100% | pseudogene (687/1129 nt) | yedN ← | putative type III secreted effector, N‑terminal fragment |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,531,418 | A→G | 5.1% | intergenic (‑185/‑45) | zipA ← / → cysZ | cell division protein ZipA/sulfate:H(+) symporter |
| RA | 2,636,200 | C→A | 15.1% | R386L (CGC→CTC) | der ← | 50S ribosomal subunit stability factor |
| RA | 2,953,617 | G→A | 8.3% | A796V (GCG→GTG) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 3,068,178 | T→A | 6.1% | S211C (AGT→TGT) | argO ← | L‑arginine exporter |
| RA | 3,375,962 | C→T | 6.0% | A365V (GCC→GTC) | dcuD → | putative transporter DcuD |
| RA | 3,448,200 | T→C | 5.2% | intergenic (‑51/+114) | rplN ← / ← rpsQ | 50S ribosomal subunit protein L14/30S ribosomal subunit protein S17 |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| JC JC | 3,651,029 | IS2 (+) +5 bp | 100% | intergenic (+367/‑258) | arsC → / → yhiS | arsenate reductase/putative uncharacterized protein YhiS |
| RA | 3,664,265 | C→G | 6.3% | S118S (TCG→TCC) | gadW ← | DNA‑binding transcriptional dual regulator GadW |
| RA | 3,815,809 | Δ1 bp | 8.0% | intergenic (‑41/+54) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
| JC | 3,815,895 | Δ14 bp | 6.8% | coding (642‑655/687 nt) | rph ← | truncated RNase PH |
| RA | 4,296,060 | C→T | 22.7% | 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 | 4,409,365 | C→A | 5.9% | R31S (CGT→AGT) | rlmB → | 23S rRNA 2'‑O‑ribose G2251 methyltransferase |
| RA | 4,516,171 | G→C | 100% | N169K (AAC→AAG) | fecA ← | ferric citrate outer membrane transporter |
| RA | 4,516,664 | C→T | 5.8% | R5H (CGC→CAC) | fecA ← | ferric citrate outer membrane transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423764–3424234 | 3424538–3424238 | 5–775 | 21 [20] | [20] 22 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 96890 | 35 (0.530) | 3 (0.050) | 3/326 | NT | 7.2% | coding (889/1083 nt) | mraY | phospho‑N‑acetylmuramoyl‑pentapeptide‑ transferase |
| ? | NC_000913 | 2769127 = | 43 (0.660) | coding (463/822 nt) | yfjQ | CP4‑57 prophage; protein YfjQ | |||||
| * | ? | NC_000913 | 1207790 = | 39 (0.590) | 51 (0.860) | 31/296 | NT | 60.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 31 (0.520) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 39 (0.590) | 30 (0.510) | 25/296 | NT | 47.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 31 (0.520) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.020) | 49 (0.760) | 30/320 | NT | 99.0% | 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 | 2060620 = | 63 (0.960) | 4 (0.060) | 4/318 | NT | 6.0% | coding (295/951 nt) | cbl | DNA‑binding transcriptional activator Cbl |
| ? | NC_000913 | 2060710 = | 64 (1.000) | coding (205/951 nt) | cbl | DNA‑binding transcriptional activator Cbl | |||||
| * | ? | NC_000913 | = 2754395 | 53 (0.810) | 4 (0.060) | 4/316 | NT | 5.8% | coding (370/477 nt) | ratA | ribosome association toxin RatA |
| ? | NC_000913 | = 2754461 | 78 (1.230) | coding (304/477 nt) | ratA | ribosome association toxin RatA | |||||
| * | ? | NC_000913 | = 2951225 | 65 (0.990) | 4 (0.060) | 4/310 | NT | 6.5% | coding (1237/1827 nt) | recD | exodeoxyribonuclease V subunit RecD |
| ? | NC_000913 | = 2951680 | 53 (0.850) | coding (782/1827 nt) | recD | exodeoxyribonuclease V subunit RecD | |||||
| * | ? | NC_000913 | 3028035 = | 54 (0.820) | 4 (0.060) | 3/312 | NT | 8.5% | coding (915/1368 nt) | ghxQ | guanine/hypoxanthine transporter GhxQ |
| ? | NC_000913 | 3028459 = | 35 (0.560) | coding (1339/1368 nt) | ghxQ | guanine/hypoxanthine transporter GhxQ | |||||
| * | ? | NC_000913 | 3041478 = | 54 (0.820) | 3 (0.050) | 3/316 | NT | 5.5% | coding (166/981 nt) | ygfZ | folate‑binding protein |
| ? | NC_000913 | 3041664 = | 51 (0.800) | coding (352/981 nt) | ygfZ | folate‑binding protein | |||||
| * | ? | NC_000913 | 3330071 = | 70 (1.060) | 4 (0.060) | 4/312 | NT | 6.6% | coding (1109/1434 nt) | dacB | peptidoglycan DD‑endopeptidase DacB |
| ? | NC_000913 | 3330183 = | 47 (0.750) | coding (1221/1434 nt) | dacB | peptidoglycan DD‑endopeptidase DacB | |||||
| * | ? | NC_000913 | 4512186 = | 67 (1.020) | 6 (0.100) | 5/312 | NT | 8.8% | coding (229/957 nt) | fecD | ferric citrate ABC transporter membrane subunit FecD |
| ? | NC_000913 | = 4623801 | 60 (0.960) | coding (317/1017 nt) | lplA | lipoate‑‑protein ligase A | |||||
| * | ? | NC_000913 | 4542682 = | 48 (0.730) | 5 (0.080) | 5/310 | NT | 8.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 65 (1.050) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 51 (0.780) | 8 (0.130) | 8/310 | NT | 12.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 65 (1.050) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||