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 | annotation | gene | description |
| RA | 55,452 | G→T | A553D (GCC→GAC) | lptD ← | lipopolysaccharide assembly protein LptD |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | 459,278 | Δ69 bp | coding (391‑459/2355 nt) | lon → | Lon protease |
| JC JC | 486,122 | IS1 (+) +8 bp | coding (362‑369/648 nt) | acrR → | DNA‑binding transcriptional repressor AcrR |
| RA | 803,662 | C→A | L54I (CTT→ATT) | ybhJ → | putative hydratase YbhJ |
| RA | 1,619,325 | G→A | G69E (GGA→GAA) | marR → | DNA‑binding transcriptional repressor MarR |
| RA | 1,903,280 | G→A | G67S (GGT→AGT) | manY → | mannose‑specific PTS enzyme IIC component |
| RA | 1,905,761 | G→A | G25D (GGT→GAT) | mntP → | Mn(2(+)) exporter |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| JC JC | 3,397,946 | IS5 (+) +4 bp | coding (430‑433/594 nt) | yhdE ← | nucleoside triphosphate pyrophosphatase YhdE |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 4,390,754 | G→T | A252A (GCC→GCA) | rsgA ← | ribosome small subunit‑dependent GTPase A |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423713–3424234 | 3424589–3424238 | 5–877 | 7 [3] | [4] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4296119–4296378 | 4296392 | 15–274 | 6 [5] | [5] 8 | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 291401 | NA (NA) | 16 (0.280) | 12/128 | 1.2 | 21.6% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 480996 | 58 (1.000) | intergenic (‑288/+258) | tomB/acrB | protein that modulates Hha toxicity/multidrug efflux pump RND permease AcrB | |||||
| * | ? | NC_000913 | = 481157 | 54 (0.930) | 15 (0.270) | 10/124 | 1.4 | 22.3% | intergenic (‑449/+97) | tomB/acrB | protein that modulates Hha toxicity/multidrug efflux pump RND permease AcrB |
| ? | NC_000913 | 1049778 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.260) | 38 (0.870) | 22/96 | 0.2 | 74.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 15 (0.340) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.260) | 28 (0.640) | 15/96 | 0.5 | 68.1% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 15 (0.340) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 80 (1.470) | 35/120 | 0.1 | 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 | = 1979270 | NA (NA) | 66 (1.140) | 32/128 | 0.1 | 43.4% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3844020 | 86 (1.480) | coding (57/1767 nt) | adeD | adenine deaminase | |||||
| * | ? | NC_000913 | 4542682 = | 45 (0.770) | 10 (0.200) | 7/110 | 1.7 | 20.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 40 (0.800) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 45 (0.770) | 19 (0.380) | 13/110 | 0.8 | 32.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 40 (0.800) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||