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 22 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 | 38.9% | 133.3 / 68.9 | 113 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,404,215 | 0 | T | G | 32.9% | 130.1 / 39.7 | 75 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 29,496 | 0 | T | A | 31.2% | 145.1 / 40.1 | 77 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,878,462 | 0 | T | C | 30.5% | 167.0 / 119.8 | 131 | D553G (GAT→GGT) | gyrB | DNA gyrase subunit B |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.9% | 338.7 / 24.4 | 154 | 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 | 27.8% | 103.7 / 22.9 | 54 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 650,809 | 0 | T | G | 27.4% | 191.0 / 19.3 | 84 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 753,125 | 0 | T | A | 27.1% | 181.5 / 34.0 | 86 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 888,014 | 0 | T | G | 27.0% | 204.9 / 16.2 | 90 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 501,575 | 0 | A | C | 26.5% | 116.7 / 10.1 | 49 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.4% | 142.0 / 31.0 | 63 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,404,218 | 0 | T | G | 25.4% | 167.9 / 15.3 | 71 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 24.5% | 241.9 / 24.8 | 94 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,098,155 | 0 | A | C | 23.7% | 224.4 / 16.7 | 94 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.2% | 317.7 / 90.7 | 155 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 501,564 | 0 | A | C | 23.2% | 135.5 / 21.0 | 56 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 1,068,173 | 0 | T | G | 22.9% | 274.0 / 26.1 | 109 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 1,550,663 | 0 | A | C | 22.6% | 157.2 / 13.0 | 62 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 4,296,155 | 0 | T | C | 21.9% | 62.7 / 14.8 | 32 | intergenic (+361/+281) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 753,114 | 0 | G | T | 20.7% | 242.6 / 16.9 | 87 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 6 (0.080) | 6/192 | 6.3 | 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 | = 4542690 | 106 (0.940) | 10 (0.100) | 7/260 | 7.5 | 8.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 119 (1.130) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2817942 | 113 (1.010) | 4 (0.040) | 4/238 | 8.5 | 3.6% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818078 = | 117 (1.220) | noncoding (58/77 nt) | argZ | tRNA‑Arg | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 5 (0.050) | 5/262 | 8.5 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 3363509 | 291 (2.590) | 4 (0.040) | 4/272 | 9.2 | 1.3% | coding (703/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3363589 = | 308 (2.800) | coding (783/2382 nt) | yhcD | putative fimbrial usher protein YhcD | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 4 (0.040) | 4/270 | 9.2 | 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 | = 1459415 | 42 (0.370) | 3 (0.030) | 3/268 | 9.8 | 4.1% | coding (362/1428 nt) | paaH | 3‑hydroxyadipyl‑CoA dehydrogenase |
| ? | NC_000913 | = 1459502 | 101 (0.930) | coding (449/1428 nt) | paaH | 3‑hydroxyadipyl‑CoA dehydrogenase | |||||
| * | ? | NC_000913 | 1459411 = | 35 (0.310) | 3 (0.030) | 3/268 | 9.8 | 4.3% | coding (358/1428 nt) | paaH | 3‑hydroxyadipyl‑CoA dehydrogenase |
| ? | NC_000913 | 1459508 = | 101 (0.930) | coding (455/1428 nt) | paaH | 3‑hydroxyadipyl‑CoA dehydrogenase | |||||
| * | ? | NC_000913 | 1237403 = | 109 (0.970) | 3 (0.030) | 3/272 | 9.8 | 3.0% | intergenic (‑162/‑168) | ycgB/dadA | PF04293 family protein YcgB/D‑amino acid dehydrogenase |
| ? | NC_000913 | = 1238281 | 89 (0.810) | coding (711/1299 nt) | dadA | D‑amino acid dehydrogenase | |||||
| * | ? | NC_000913 | 164055 = | 125 (1.110) | 3 (0.030) | 3/272 | 9.8 | 2.6% | coding (1951/2430 nt) | hrpB | putative ATP‑dependent RNA helicase HrpB |
| ? | NC_000913 | 164133 = | 102 (0.930) | coding (2029/2430 nt) | hrpB | putative ATP‑dependent RNA helicase HrpB | |||||