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 | 40.4% | 104.5 / 64.3 | 94 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 34.2% | 90.3 / 28.2 | 41 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,207 | 0 | T | C | 34.0% | 68.1 / 22.6 | 47 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,550,663 | 0 | A | C | 31.8% | 102.3 / 22.0 | 63 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 3,556,205 | 0 | A | C | 30.4% | 76.8 / 19.4 | 46 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 29,496 | 0 | T | A | 28.0% | 102.3 / 22.8 | 50 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,296,060 | 0 | C | T | 27.8% | 180.5 / 69.3 | 97 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 445,558 | 0 | A | C | 27.8% | 94.3 / 25.4 | 54 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 2,628,625 | 0 | A | C | 27.3% | 79.6 / 14.7 | 44 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 650,809 | 0 | T | G | 26.9% | 187.5 / 23.1 | 93 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,667,126 | 0 | A | C | 24.7% | 159.8 / 16.3 | 81 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 24.3% | 70.0 / 13.3 | 37 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 23.8% | 89.7 / 11.0 | 42 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.8% | 160.9 / 37.8 | 80 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 23.4% | 238.1 / 13.1 | 111 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 646,747 | 0 | T | G | 23.4% | 93.1 / 19.1 | 47 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 372,640 | 0 | T | G | 22.4% | 119.8 / 12.5 | 58 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| 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 | 4542682 = | 101 (0.980) | 10 (0.100) | 10/258 | 5.7 | 9.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 103 (1.070) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 92 (0.890) | 10 (0.100) | 9/258 | 6.0 | 9.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 100 (1.040) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 967030 = | 121 (1.170) | 4 (0.040) | 4/256 | 8.1 | 3.4% | coding (410/1749 nt) | msbA | ATP‑binding lipopolysaccharide transport protein |
| ? | NC_000913 | = 967026 | 115 (1.200) | coding (406/1749 nt) | msbA | ATP‑binding lipopolysaccharide transport protein | |||||
| * | ? | NC_000913 | = 160454 | 151 (1.470) | 4 (0.040) | 4/274 | 8.5 | 2.6% | coding (151/456 nt) | dksA | RNA polymerase‑binding transcription factor DksA |
| ? | NC_000913 | = 160568 | 148 (1.450) | coding (37/456 nt) | dksA | RNA polymerase‑binding transcription factor DksA | |||||
| * | ? | NC_000913 | 2023462 = | 97 (0.940) | 3 (0.030) | 3/268 | 9.0 | 3.1% | coding (570/786 nt) | fliR | flagellar biosynthesis protein FliR |
| ? | NC_000913 | = 2023615 | 91 (0.910) | coding (723/786 nt) | fliR | flagellar biosynthesis protein FliR | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 4 (0.040) | 3/272 | 9.0 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 275089 | NA (NA) | noncoding (61/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1979486 = | 74 (0.720) | 23 (0.220) | 3/276 | 9.1 | 23.7% | 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 | |||||