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 | 4,604,344 | 0 | C | T | 42.5% | 77.8 / 62.4 | 94 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,296,060 | 0 | C | T | 38.3% | 87.3 / 81.9 | 81 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 646,747 | 0 | T | G | 31.1% | 72.5 / 24.7 | 45 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 28.0% | 79.7 / 23.0 | 50 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.3% | 146.6 / 24.6 | 57 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 25.8% | 180.4 / 11.2 | 90 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.4% | 146.5 / 18.0 | 67 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 445,558 | 0 | A | C | 24.4% | 79.6 / 16.4 | 41 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 786,855 | 0 | A | C | 24.1% | 122.8 / 10.3 | 54 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 4,098,155 | 0 | A | C | 23.7% | 200.0 / 14.3 | 93 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 4,111,752 | 0 | T | C | 22.7% | 130.5 / 12.7 | 67 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,350,853 | 0 | A | C | 22.2% | 124.8 / 14.3 | 54 | S725A (TCA→GCA) | arcB | sensory histidine kinase ArcB |
| * | NC_000913 | 29,496 | 0 | T | A | 21.7% | 151.1 / 16.2 | 60 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,926,366 | 0 | A | C | 21.1% | 290.1 / 21.9 | 123 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.1% | 130.5 / 16.8 | 57 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,161,148 | 0 | G | A | 20.8% | 220.3 / 21.5 | 101 | E28K (GAA→AAA) | fabR | DNA‑binding transcriptional repressor FabR |
| * | NC_000913 | 2,583,424 | 0 | T | G | 20.0% | 207.0 / 11.7 | 85 | T19P (ACC→CCC) | nudK | GDP‑mannose hydrolase |
| 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 | = 1207805 | 82 (0.880) | 16 (0.190) | 15/246 | 3.5 | 18.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 73 (0.890) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 86 (0.920) | 15 (0.170) | 15/260 | 3.7 | 15.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 87 (1.000) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 79 (0.850) | 11 (0.130) | 10/260 | 5.0 | 12.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 86 (0.990) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1979489 | 97 (1.040) | 10 (0.110) | 7/278 | 6.3 | 9.3% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 3 (0.050) | 3/192 | 6.6 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1979489 | 97 (1.040) | 5 (0.050) | 5/278 | 7.2 | 4.9% | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2067353 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1979486 = | 99 (1.060) | 27 (0.290) | 4/278 | 7.7 | 21.4% | intergenic (‑271/‑267) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||