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 28 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 445,558 | 0 | A | C | 46.3% | 24.4 / 34.9 | 41 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,365,437 | 0 | C | T | 45.0% | 112.5 / inf | 298 | pseudogene (253/371 nt) | yhcE | putative uncharacterized protein YhcE |
| * | NC_000913 | 1,775,467 | 0 | A | C | 35.7% | 57.2 / 11.5 | 42 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 35.7% | 66.0 / 15.7 | 42 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,604,344 | 0 | C | T | 35.7% | 131.0 / 54.2 | 98 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 802,118 | 0 | A | C | 33.3% | 78.8 / 12.1 | 45 | T78P (ACC→CCC) | ybhI | putative tricarboxylate transporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 33.0% | 129.8 / 78.6 | 91 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.2% | 231.0 / 21.7 | 130 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,556,205 | 0 | A | C | 31.1% | 82.1 / 13.7 | 45 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 102,266 | 0 | A | G | 30.8% | 115.7 / 73.9 | 91 | T12A (ACC→GCC) | ddlB | D‑alanine‑‑D‑alanine ligase B |
| * | NC_000913 | 1,825,061 | 0 | G | A | 30.6% | 60.9 / 10.9 | 36 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,326,450 | 0 | T | G | 30.5% | 102.7 / 31.1 | 59 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 29.2% | 86.0 / 14.0 | 48 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.2% | 95.6 / 14.3 | 39 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 501,575 | 0 | A | C | 27.3% | 115.1 / 16.2 | 55 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 372,640 | 0 | T | G | 26.1% | 148.7 / 15.3 | 69 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 4,209,827 | 0 | T | G | 24.1% | 99.3 / 10.5 | 58 | noncoding (54/76 nt) | gltV | tRNA‑Glu |
| * | NC_000913 | 753,125 | 0 | T | A | 24.1% | 138.1 / 14.0 | 54 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 22.9% | 188.3 / 24.7 | 83 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,350,853 | 0 | A | C | 22.9% | 163.6 / 18.4 | 70 | S725A (TCA→GCA) | arcB | sensory histidine kinase ArcB |
| Marginal new junction evidence (lowest skew 10 of 38 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 90 (0.900) | 19 (0.200) | 18/258 | 2.7 | 15.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 125 (1.340) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375203 = | NA (NA) | 22 (0.280) | 12/216 | 3.2 | NA | noncoding (17/36 nt) | other | REP31f |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375082 = | NA (NA) | 23 (0.270) | 11/238 | 3.7 | NA | intergenic (+201/‑377) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 17 (0.170) +T |
13/274 | 3.8 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375183 = | NA (NA) | 19 (0.220) | 10/238 | 4.0 | NA | intergenic (+302/‑276) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 375124 = | NA (NA) | 16 (0.230) | 7/192 | 4.1 | 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 | |||||
| * | ? | NC_000913 | = 4542690 | 78 (0.780) | 11 (0.120) | 10/258 | 4.2 | 10.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 125 (1.340) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 9 (0.110) | 8/224 | 4.3 | 10.2% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 79 (0.980) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 374987 = | NA (NA) | 11 (0.120) | 8/250 | 4.6 | NA | noncoding (31/36 nt) | other | REP31b |
| ? | NC_000913 | 377366 = | NA (NA) | noncoding (31/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 374958 | NA (NA) | 6 (0.080) | 5/202 | 4.9 | NA | noncoding (28/34 nt) | other | REP31a |
| ? | NC_000913 | = 377392 | NA (NA) | noncoding (31/34 nt) | other | REP32b | |||||