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 | 48.6% | 35.2 / 60.4 | 70 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 753,125 | 0 | T | A | 31.8% | 88.6 / 19.6 | 44 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 175,694 | 0 | T | G | 31.6% | 81.9 / 23.1 | 57 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 2,001,918 | 0 | A | C | 29.1% | 96.4 / 21.2 | 55 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,435 | 0 | C | T | 29.0% | 47.7 / 14.4 | 31 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,628,625 | 0 | A | C | 28.9% | 60.5 / 14.1 | 38 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 2,326,450 | 0 | T | G | 28.3% | 89.2 / 25.1 | 53 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 650,809 | 0 | T | G | 26.4% | 91.9 / 13.9 | 53 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 26.0% | 90.6 / 16.8 | 50 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 2,664,896 | 0 | T | G | 23.3% | 83.0 / 13.1 | 44 | G169G (GGT→GGG) | yfhR | putative peptidase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.4% | 175.7 / 45.1 | 85 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,531,440 | 0 | A | C | 21.3% | 132.3 / 10.6 | 61 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 1,068,173 | 0 | T | G | 21.3% | 97.0 / 11.0 | 47 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 29,496 | 0 | T | A | 20.9% | 108.2 / 12.3 | 43 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 375,168 | 0 | G | A | 20.4% | 124.4 / 23.4 | 55 | intergenic (+287/‑291) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 4,614,496 | 0 | C | T | 20.0% | 97.9 / 14.6 | 40 | intergenic (+236/+184) | yjjV/yjjW | putative DNase YjjV/putative glycyl‑radical enzyme activating enzyme YjjW |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 51 (0.750) | 18 (0.280) | 14/258 | 3.0 | 26.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 53 (0.830) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 53 (0.780) | 16 (0.250) | 12/258 | 3.5 | 23.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 55 (0.860) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 6 (0.090) | 5/260 | 5.8 | 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 | = 2556343 | 65 (0.950) | 4 (0.060) | 4/252 | 6.1 | 7.0% | coding (58/660 nt) | eutL | putative structural protein, ethanolamine utilization microcompartment |
| ? | NC_000913 | = 2558100 | 47 (0.750) | coding (580/1362 nt) | eutB | ethanolamine ammonia‑lyase subunit alpha | |||||
| * | ? | NC_000913 | = 2683557 | 61 (0.890) | 6 (0.090) | 4/264 | 6.3 | 9.1% | coding (695/1194 nt) | yphH | putative DNA‑binding transcriptional regulator, NAGC‑like |
| ? | NC_000913 | = 2683637 | 62 (0.950) | coding (775/1194 nt) | yphH | putative DNA‑binding transcriptional regulator, NAGC‑like | |||||
| * | ? | NC_000913 | 1769517 = | 45 (0.660) | 3 (0.050) | 3/256 | 6.7 | 6.6% | coding (444/1113 nt) | ydiK | putative transporter YdiK |
| ? | NC_000913 | = 1769513 | 43 (0.680) | coding (440/1113 nt) | ydiK | putative transporter YdiK | |||||
| * | ? | NC_000913 | = 153209 | 77 (1.130) | 3 (0.050) | 3/262 | 6.8 | 4.1% | coding (2218/2598 nt) | htrE | putative fimbrial usher protein HtrE |
| ? | NC_000913 | = 153237 | 67 (1.030) | coding (2190/2598 nt) | htrE | putative fimbrial usher protein HtrE | |||||
| * | ? | NC_000913 | 4122668 = | 60 (0.880) | 4 (0.060) | 3/274 | 7.0 | 7.2% | coding (672/960 nt) | ftsN | cell division protein FtsN |
| ? | NC_000913 | 4122742 = | 44 (0.650) | coding (598/960 nt) | ftsN | cell division protein FtsN | |||||
| * | ? | NC_000913 | 4602063 = | 88 (1.290) | 3 (0.040) | 3/276 | 7.1 | 3.3% | coding (35/474 nt) | yjjB | putative succinate exporter YjjB |
| ? | NC_000913 | = 4614271 | NA (NA) | noncoding (21/34 nt) | other | REP352a | |||||