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 | 39.5% | 42.1 / 24.9 | 43 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 37.8% | 35.9 / 25.2 | 37 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,556,207 | 0 | T | C | 33.3% | 42.3 / 11.3 | 30 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 32.4% | 55.3 / 10.7 | 37 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.4% | 65.3 / 13.8 | 35 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 374,972 | 0 | T | C | 31.2% | 69.6 / 52.0 | 64 | intergenic (+91/‑487) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 374,986 | 0 | T | C | 31.2% | 69.9 / 55.2 | 64 | intergenic (+105/‑473) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 30.4% | 70.8 / 34.2 | 46 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,429,984 | 0 | T | G | 26.5% | 116.7 / 11.1 | 49 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,404,215 | 0 | T | G | 24.4% | 93.7 / 11.1 | 41 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.3% | 96.2 / 19.3 | 43 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 56 (1.030) | 10 (0.200) | 10/258 | 3.1 | 15.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 61 (1.200) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 10 (0.200) | 7/256 | 3.9 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 8 (0.150) +T |
8/274 | 3.9 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 374958 | NA (NA) | 6 (0.150) | 4/202 | 4.2 | NA | noncoding (28/34 nt) | other | REP31a |
| ? | NC_000913 | = 377392 | NA (NA) | noncoding (31/34 nt) | other | REP32b | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 7 (0.180) | 4/202 | 4.2 | 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 | |||||
| * | ? | NC_000913 | 4542682 = | 63 (1.150) | 6 (0.120) | 6/258 | 4.3 | 9.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 61 (1.200) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 248286 | NA (NA) | 4 (0.110) +49 bp |
3/178 | 4.3 | NA | intergenic (+152/+72) | rayT/lfhA | REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment |
| ? | NC_000913 | 2340313 = | NA (NA) | intergenic (+24/+104) | ubiG/yfaL | bifunctional 3‑demethylubiquinone‑8 3‑O‑methyltransferase and 2‑octaprenyl‑6‑hydroxyphenol methylase/putative autotransporter adhesin YfaL | |||||
| * | ? | NC_000913 | = 173542 | NA (NA) | 4 (0.110) +49 bp |
3/178 | 4.3 | NA | intergenic (+98/+60) | fhuB/hemL | iron(III) hydroxamate ABC transporter membrane subunit/glutamate‑1‑semialdehyde aminotransferase |
| ? | NC_000913 | 2340313 = | NA (NA) | intergenic (+24/+104) | ubiG/yfaL | bifunctional 3‑demethylubiquinone‑8 3‑O‑methyltransferase and 2‑octaprenyl‑6‑hydroxyphenol methylase/putative autotransporter adhesin YfaL | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 8 (0.170) +GAACGCCTTATCCGGT |
5/244 | 4.5 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 377321 = | NA (NA) | 7 (0.130) | 5/268 | 4.8 | NA | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | = 508817 | NA (NA) | noncoding (2/34 nt) | other | REP48e | |||||