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 21 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 39.7% | 79.7 / 39.9 | 68 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,101,514 | 0 | G | T | 37.7% | 104.5 / 31.0 | 53 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,825,061 | 0 | G | A | 34.9% | 55.8 / 20.9 | 43 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.1% | 185.6 / 10.7 | 93 | 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 | 29.2% | 70.7 / 22.4 | 48 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,559,329 | 0 | G | A | 29.2% | 70.6 / 31.9 | 48 | W354* (TGG→TGA) | rtcR | DNA‑binding transcriptional activator RtcR |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.9% | 108.1 / 20.3 | 45 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.8% | 93.7 / 19.1 | 52 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.6% | 193.2 / 83.4 | 112 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,550,663 | 0 | A | C | 26.1% | 92.6 / 10.4 | 46 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 2,337,434 | 0 | A | G | 25.0% | 92.5 / 29.8 | 56 | F663L (TTC→CTC) | gyrA | DNA gyrase subunit A |
| * | NC_000913 | 4,098,155 | 0 | A | C | 25.0% | 220.5 / 18.3 | 104 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 3,915,866 | 0 | T | G | 24.6% | 134.9 / 10.3 | 62 | Y36S (TAC→TCC) | atpC | ATP synthase F1 complex subunit epsilon |
| * | NC_000913 | 29,496 | 0 | T | A | 23.9% | 115.5 / 13.2 | 46 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 22.5% | 184.4 / 16.7 | 71 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 646,747 | 0 | T | G | 22.2% | 96.3 / 16.2 | 45 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,161,148 | 0 | G | A | 21.8% | 160.4 / 15.1 | 78 | E28K (GAA→AAA) | fabR | DNA‑binding transcriptional repressor FabR |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.5% | 147.3 / 23.4 | 65 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 21.2% | 146.8 / 10.7 | 66 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 1,068,173 | 0 | T | G | 21.1% | 170.3 / 12.5 | 71 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| Marginal new junction evidence (lowest skew 10 of 24 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 15 (0.230) | 11/190 | 3.6 | 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 | 375102 = | NA (NA) | 17 (0.230) | 9/216 | 4.7 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 15 (0.200) | 8/216 | 5.0 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 4373261 = | NA (NA) | 13 (0.170) | 8/226 | 5.2 | 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 | 4373295 = | NA (NA) | 17 (0.190) | 9/256 | 5.4 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 5 (0.070) | 5/224 | 6.4 | 5.3% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 89 (1.160) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 375266 | NA (NA) | 5 (0.060) | 5/238 | 6.6 | NA | noncoding (33/34 nt) | other | REP31g |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 555833 | 91 (0.960) | 5 (0.060) | 5/244 | 6.7 | 5.5% | coding (1223/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 556784 | 93 (1.110) | coding (90/213 nt) | ybcJ | putative RNA‑binding protein YbcJ | |||||
| * | ? | NC_000913 | 3231254 = | NA (NA) | 6 (0.080) | 4/224 | 6.9 | NA | noncoding (2/34 nt) | other | REP231a |
| ? | NC_000913 | 3234722 = | NA (NA) | noncoding (3/34 nt) | other | REP233b | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 3 (0.040) | 3/202 | 7.0 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||