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 | 44.4% | 78.4 / 69.9 | 90 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 29,496 | 0 | T | A | 39.6% | 72.6 / 34.9 | 53 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 372,640 | 0 | T | G | 37.5% | 75.6 / 23.6 | 56 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 36.5% | 70.7 / 29.2 | 52 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.9% | 240.3 / 17.1 | 124 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.2% | 85.1 / 23.0 | 53 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,404,218 | 0 | T | G | 30.0% | 94.1 / 12.1 | 50 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 650,809 | 0 | T | G | 29.3% | 106.4 / 11.7 | 58 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,628,649 | 0 | A | C | 29.0% | 137.6 / 19.4 | 69 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.8% | 144.3 / 28.9 | 59 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 27.0% | 66.7 / 13.6 | 37 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 1,068,173 | 0 | T | G | 24.4% | 183.7 / 15.1 | 83 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 175,694 | 0 | T | G | 23.9% | 194.3 / 16.0 | 94 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 4,442,146 | 0 | A | G | 23.4% | 183.3 / 17.5 | 94 | S11P (TCC→CCC) | msrA | methionine sulfoxide reductase A |
| * | NC_000913 | 376,401 | 0 | T | G | 23.4% | 143.3 / 13.1 | 77 | L315V (TTG→GTG) | mhpT | 3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 23.4% | 181.3 / 17.9 | 77 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 646,747 | 0 | T | G | 22.9% | 109.1 / 12.0 | 48 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 21.5% | 269.8 / 17.0 | 121 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| Marginal new junction evidence (lowest skew 10 of 33 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 62 (0.670) | 17 (0.210) | 14/246 | 4.0 | 23.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 54 (0.660) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 4542682 = | 66 (0.710) | 13 (0.150) | 12/260 | 4.8 | 14.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 89 (1.030) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 13 (0.170) | 6/226 | 6.2 | 15.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 69 (0.920) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 2518036 = | 78 (0.840) | 7 (0.110) +41 bp |
4/196 | 6.5 | 12.2% | intergenic (‑204/+5) | pdeA/alaX | putative c‑di‑GMP phosphodiesterase PdeA/tRNA‑Ala |
| ? | NC_000913 | 2521180 = | 65 (0.700) | noncoding (8/76 nt) | valY | tRNA‑Val | |||||
| * | ? | NC_000913 | 2518036 = | 78 (0.840) | 7 (0.110) +41 bp |
4/196 | 6.5 | 12.2% | intergenic (‑204/+5) | pdeA/alaX | putative c‑di‑GMP phosphodiesterase PdeA/tRNA‑Ala |
| ? | NC_000913 | 2521058 = | 66 (0.710) | noncoding (8/76 nt) | valX | tRNA‑Val | |||||
| * | ? | NC_000913 | 781075 = | 114 (1.230) | 7 (0.110) +41 bp |
4/196 | 6.5 | 9.4% | noncoding (8/76 nt) | valZ | tRNA‑Val |
| ? | NC_000913 | 2518036 = | 78 (0.840) | intergenic (‑204/+5) | pdeA/alaX | putative c‑di‑GMP phosphodiesterase PdeA/tRNA‑Ala | |||||
| * | ? | NC_000913 | 2514273 = | NA (NA) | 5 (0.070) | 5/226 | 6.7 | 7.2% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 2515618 = | 64 (0.850) | intergenic (+175/+25) | insL‑3/pdeA | putative IS186/IS421 transposase/putative c‑di‑GMP phosphodiesterase PdeA | |||||
| * | ? | NC_000913 | = 608002 | 101 (1.090) | 6 (0.070) | 6/262 | 7.0 | 5.9% | intergenic (+14/‑63) | hokE/insL‑2 | protein HokE/IS186/IS421 transposase |
| ? | NC_000913 | = 609355 | NA (NA) | intergenic (+178/+104) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 2518036 = | 78 (0.840) | 6 (0.090) +41 bp |
3/196 | 7.1 | 10.4% | intergenic (‑204/+5) | pdeA/alaX | putative c‑di‑GMP phosphodiesterase PdeA/tRNA‑Ala |
| ? | NC_000913 | 2520938 = | 69 (0.750) | noncoding (8/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | 780772 = | 80 (0.870) | 6 (0.090) +41 bp |
3/196 | 7.1 | 9.8% | noncoding (8/76 nt) | valT | tRNA‑Val |
| ? | NC_000913 | 2518036 = | 78 (0.840) | intergenic (‑204/+5) | pdeA/alaX | putative c‑di‑GMP phosphodiesterase PdeA/tRNA‑Ala | |||||