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 | 38.9% | 152.4 / 99.3 | 144 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 32.8% | 224.2 / 20.9 | 119 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,825,061 | 0 | G | A | 30.2% | 70.5 / 15.7 | 43 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.7% | 179.0 / 52.6 | 94 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 26.0% | 152.4 / 23.1 | 73 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,207 | 0 | T | C | 25.8% | 122.7 / 14.0 | 62 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 25.0% | 190.5 / 28.8 | 69 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 372,640 | 0 | T | G | 24.7% | 156.9 / 16.1 | 73 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 650,809 | 0 | T | G | 24.7% | 152.7 / 20.1 | 73 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 646,747 | 0 | T | G | 23.5% | 172.5 / 39.5 | 82 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.4% | 251.4 / 72.6 | 124 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,101,507 | 0 | T | G | 23.3% | 194.6 / 15.7 | 90 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 29,496 | 0 | T | A | 23.3% | 171.6 / 28.9 | 73 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 786,855 | 0 | A | C | 21.1% | 173.1 / 16.1 | 71 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 2,628,625 | 0 | A | C | 20.8% | 129.4 / 12.2 | 53 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 64 (0.520) | 19 (0.170) | 16/258 | 4.4 | 20.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 92 (0.800) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 59 (0.480) | 16 (0.140) | 15/258 | 4.7 | 17.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 92 (0.800) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1207790 = | 135 (1.100) | 13 (0.120) | 13/244 | 4.9 | 10.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 105 (0.970) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 9 (0.110) | 9/190 | 4.9 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1207805 | 120 (0.980) | 9 (0.080) | 9/244 | 6.1 | 7.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 104 (0.960) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 2406540 | 114 (1.060) | 17 (0.150) +GCGGCAGCT |
5/224 | 7.3 | 12.2% | coding (102/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA |
| ? | NC_000913 | 2406541 = | 133 (1.090) | coding (101/939 nt) | lrhA | DNA‑binding transcriptional dual regulator LrhA | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 5 (0.040) | 5/268 | 8.1 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377387 | NA (NA) | intergenic (+76/+148) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 3213217 | 154 (1.260) | 5 (0.040) | 5/274 | 8.2 | 3.1% | coding (171/1842 nt) | rpoD | RNA polymerase, sigma 70 (sigma D) factor |
| ? | NC_000913 | 3213224 = | 162 (1.330) | coding (178/1842 nt) | rpoD | RNA polymerase, sigma 70 (sigma D) factor | |||||
| * | ? | NC_000913 | 1552188 = | NA (NA) | 4 (0.030) | 4/266 | 8.6 | NA | intergenic (+197/+210) | fdnI/yddM | formate dehydrogenase N subunit gamma/putative DNA‑binding transcriptional regulator YddM |
| ? | NC_000913 | 1552323 = | NA (NA) | noncoding (24/29 nt) | other | REPv121b | |||||
| * | ? | NC_000913 | 92847 = | 98 (0.800) | 3 (0.030) | 3/256 | 9.0 | 3.1% | coding (1435/1767 nt) | ftsI | peptidoglycan DD‑transpeptidase FtsI |
| ? | NC_000913 | = 92843 | 96 (0.850) | coding (1431/1767 nt) | ftsI | peptidoglycan DD‑transpeptidase FtsI | |||||