mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 555 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 213,341 | 0 | A | G | 50.0% | 58.7 / 31.6 | 60 | G337G (GGA→GGG) | tilS | tRNA(Ile)‑lysidine synthetase |
| * | NC_000913 | 1,413,735 | 0 | A | T | 49.4% | 64.5 / 72.4 | 88 | Y2* (TAT→TAA) | ydaC | DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein |
| * | NC_000913 | 1,649,295 | 0 | T | G | 47.9% | 109.9 / 21.7 | 71 | intergenic (+254/‑314) | ydfC/dicB | uncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein |
| * | NC_000913 | 357,880 | 0 | T | C | 46.9% | 74.3 / 18.0 | 64 | K271E (AAA→GAA) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 2,984,441 | 0 | A | C | 46.6% | 125.9 / 18.9 | 73 | G384G (GGT→GGG) | yqeF | short chain acyltransferase |
| * | NC_000913 | 1,622,816 | 0 | G | A | 44.7% | 70.6 / 91.7 | 94 | intergenic (+75/+144) | yneM/dgcZ | inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing |
| * | NC_000913 | 3,850,007 | 0 | G | A | 43.2% | 85.1 / 39.2 | 74 | P44S (CCG→TCG) | uhpB | sensory histidine kinase in two‑component regulatory sytem with UhpA |
| * | NC_000913 | 3,206,435 | 0 | C | T | 42.9% | 100.7 / 58.9 | 91 | intergenic (‑179/‑28) | ttdR/ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| * | NC_000913 | 599,576 | 0 | T | G | 42.0% | 155.6 / 13.9 | 82 | V288G (GTG→GGG) | cusA | copper/silver efflux system, membrane component |
| * | NC_000913 | 3,443,277 | 0 | A | C | 41.8% | 178.1 / 22.5 | 98 | V274G (GTA→GGA) | secY | preprotein translocase membrane subunit |
| * | NC_000913 | 29,496 | 0 | T | A | 41.8% | 138.7 / 56.0 | 103 | intergenic (+301/‑155) | dapB/carA | dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| * | NC_000913 | 1,376,505 | 0 | A | C | 41.2% | 146.3 / 11.8 | 81 | T158P (ACC→CCC) | ycjR | putative TIM alpha/beta barrel enzyme |
| * | NC_000913 | 3,423,297 | 0 | G | C | 41.1% | 190.8 / 51.7 | 112 | intergenic (+103/+126) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| * | NC_000913 | 1,004,648 | 0 | T | A | 40.8% | 113.1 / 42.0 | 72 | N234K (AAT→AAA) | ycbF | putative periplasmic pilin chaperone |
| * | NC_000913 | 5,159 | 0 | G | A | 40.7% | 143.7 / 64.4 | 118 | intergenic (+139/‑75) | thrC/yaaX | L‑threonine synthase/DUF2502 family putative periplasmic protein |
| * | NC_000913 | 357,890 | 0 | C | A | 40.7% | 53.9 / 27.0 | 59 | L267F (TTG→TTT) | cynR | transcriptional activator of cyn operon; autorepressor |
| * | NC_000913 | 4,378,802 | 0 | A | C | 40.7% | 172.3 / 18.7 | 91 | V48G (GTA→GGA) | ampC | penicillin‑binding protein; beta‑lactamase, intrinsically weak |
| * | NC_000913 | 1,510,395 | 0 | C | A | 40.6% | 166.5 / 49.8 | 101 | S131R (AGC→AGA) | ydcR | putative DNA‑binding transcriptional regulator and putative aminotransferase |
| * | NC_000913 | 1,413,751 | 0 | A | C | 40.5% | 122.7 / 33.3 | 85 | N59K (AAT→AAG) | ralR | Rac prophage; restriction alleviation protein |
| * | NC_000913 | 298,960 | 0 | A | C | 40.3% | 133.6 / 13.0 | 68 | Y659D (TAT→GAT) | paoC | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 58 (0.630) | 17 (0.210) | 17/266 | 6.4 | 21.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 71 (0.870) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 57 (0.620) | 16 (0.200) | 14/266 | 7.4 | 21.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 68 (0.830) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1947865 | 81 (0.880) | 4 (0.050) | 4/274 | 12.7 | 5.0% | coding (287/741 nt) | yebC | UPF0082 family protein |
| ? | NC_000913 | = 1947853 | 77 (0.910) | coding (299/741 nt) | yebC | UPF0082 family protein | |||||
| * | ? | NC_000913 | = 1404589 | 101 (1.100) | 4 (0.050) | 4/282 | 13.0 | 3.9% | intergenic (‑24/‑152) | abgA/abgR | p‑aminobenzoyl‑glutamate hydrolase, A subunit/putative DNA‑binding transcriptional regulator of abgABT operon |
| ? | NC_000913 | = 1404615 | 99 (1.140) | intergenic (‑50/‑126) | abgA/abgR | p‑aminobenzoyl‑glutamate hydrolase, A subunit/putative DNA‑binding transcriptional regulator of abgABT operon | |||||
| * | ? | NC_000913 | = 3270571 | 81 (0.880) | 4 (0.050) | 4/286 | 13.1 | 4.9% | intergenic (+969/+54) | yhaC/garK | pentapetide repeats‑related protein/glycerate kinase I |
| ? | NC_000913 | = 3270587 | 78 (0.880) | intergenic (+985/+38) | yhaC/garK | pentapetide repeats‑related protein/glycerate kinase I | |||||
| * | ? | NC_000913 | = 3788702 | 91 (0.990) | 4 (0.040) | 4/290 | 13.2 | 4.5% | coding (602/960 nt) | yibQ | putative polysaccharide deacetylase |
| ? | NC_000913 | = 3788713 | 82 (0.920) | coding (613/960 nt) | yibQ | putative polysaccharide deacetylase | |||||
| * | ? | NC_000913 | = 1470402 | NA (NA) | 4 (0.040) | 4/290 | 13.2 | NA | noncoding (1107/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1470416 | NA (NA) | noncoding (1121/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 279997 | 73 (0.790) | 4 (0.040) | 4/290 | 13.2 | 5.3% | noncoding (67/181 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1470416 | NA (NA) | noncoding (1121/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 271647 | 97 (1.060) | 4 (0.040) | 4/290 | 13.2 | 4.1% | noncoding (1107/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1470416 | NA (NA) | noncoding (1121/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 1618675 | 103 (1.120) | 4 (0.040) | 4/292 | 13.3 | 3.7% | coding (234/666 nt) | marC | UPF0056 family inner membrane protein |
| ? | NC_000913 | = 1618697 | 106 (1.180) | coding (212/666 nt) | marC | UPF0056 family inner membrane protein | |||||