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 (highest frequency 20 of 24 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,420,787 | 1 | . | G | 42.6% | 6.0 / 108.8 | 54 | coding (104/423 nt) | ydaT | Rac prophage; protein YdaT |
| * | NC_000913 | 4,604,344 | 0 | C | T | 41.7% | 53.3 / 42.1 | 60 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 34.2% | 58.6 / 13.9 | 38 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 2,628,625 | 0 | A | C | 32.0% | 90.7 / 14.6 | 50 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.9% | 114.6 / 10.3 | 69 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.7% | 90.1 / 15.0 | 37 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,404,215 | 0 | T | G | 28.8% | 114.7 / 19.2 | 59 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 372,640 | 0 | T | G | 28.3% | 105.2 / 19.0 | 60 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 650,809 | 0 | T | G | 28.3% | 93.2 / 13.5 | 53 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.1% | 102.8 / 26.1 | 57 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,645,034 | 0 | A | C | 27.1% | 91.2 / 12.8 | 48 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 1,335,691 | 0 | T | G | 26.4% | 136.4 / 13.1 | 72 | intergenic (+24/‑140) | ymiC/acnA | protein YmiC/aconitate hydratase 1 |
| * | NC_000913 | 1,825,061 | 0 | G | A | 25.6% | 73.3 / 10.7 | 39 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 646,747 | 0 | T | G | 25.0% | 97.9 / 16.6 | 48 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 25.0% | 77.5 / 16.7 | 44 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 24.5% | 120.5 / 13.9 | 49 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 377,492 | 0 | G | A | 24.4% | 196.5 / 48.1 | 90 | intergenic (+181/+43) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 4,429,984 | 0 | T | G | 24.2% | 149.3 / 11.9 | 66 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 4,161,148 | 0 | G | A | 23.6% | 115.2 / 11.2 | 55 | E28K (GAA→AAA) | fabR | DNA‑binding transcriptional repressor FabR |
| * | NC_000913 | 29,496 | 0 | T | A | 23.4% | 117.1 / 14.1 | 47 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| Marginal new junction evidence (lowest skew 10 of 60 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 375203 = | NA (NA) | 39 (0.620) | 13/216 | 3.0 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 51 (0.810) | 13/216 | 3.0 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 42 (0.760) | 11/190 | 3.0 | 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 | = 4542690 | 63 (0.780) | 13 (0.170) | 12/258 | 4.0 | 15.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 79 (1.050) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 13 (0.200) | 9/224 | 4.2 | 12.9% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 88 (1.350) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 17 (0.210) +T |
12/274 | 4.2 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 37 (0.660) | 7/192 | 4.3 | NA | intergenic (+142/‑436) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 377353 = | NA (NA) | 10 (0.160) +30 bp |
8/216 | 4.4 | NA | noncoding (18/37 nt) | other | REP32a |
| ? | NC_000913 | 4325850 = | NA (NA) | intergenic (‑109/+549) | yjdN/yjdM | conserved protein YjdN/conserved protein YjdM | |||||
| * | ? | NC_000913 | 4373261 = | NA (NA) | 20 (0.300) | 8/226 | 4.6 | NA | intergenic (+99/+104) | yjeI/yjeJ | DUF4156 domain‑containing lipoprotein YjeI/protein YjeJ |
| ? | NC_000913 | 4374533 = | NA (NA) | intergenic (‑299/+96) | yjeJ/epmB | protein YjeJ/lysine 2,3‑aminomutase | |||||
| * | ? | NC_000913 | 375124 = | NA (NA) | 9 (0.160) | 6/192 | 4.6 | NA | intergenic (+243/‑335) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||