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 24 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 | 39.0% | 113.8 / 64.4 | 100 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 36.7% | 121.6 / 44.5 | 79 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 29,496 | 0 | T | A | 33.3% | 108.8 / 34.8 | 66 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 501,575 | 0 | A | C | 31.5% | 96.6 / 25.9 | 54 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 753,125 | 0 | T | A | 31.4% | 152.5 / 39.4 | 86 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 372,640 | 0 | T | G | 31.1% | 136.2 / 24.1 | 74 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 3,556,205 | 0 | A | C | 29.8% | 97.4 / 14.0 | 47 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 29.4% | 118.0 / 26.7 | 51 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,111,752 | 0 | T | C | 28.6% | 104.8 / 11.0 | 56 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 501,564 | 0 | A | C | 28.0% | 96.8 / 26.2 | 50 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,556,207 | 0 | T | C | 27.7% | 88.6 / 12.3 | 47 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 26.8% | 104.9 / 17.8 | 56 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 501,572 | 0 | A | C | 26.4% | 115.7 / 13.5 | 53 | V556G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 1,491,098 | 0 | A | C | 25.6% | 195.4 / 19.3 | 90 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 1,491,103 | 0 | A | C | 24.2% | 204.3 / 18.9 | 91 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.0% | 248.9 / 73.4 | 125 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 753,121 | 0 | C | A | 23.6% | 229.0 / 15.6 | 90 | intergenic (‑326/+64) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 753,114 | 0 | G | T | 22.9% | 254.4 / 16.3 | 96 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,335,691 | 0 | T | G | 22.7% | 217.7 / 17.5 | 97 | intergenic (+24/‑140) | ymiC/acnA | protein YmiC/aconitate hydratase 1 |
| * | NC_000913 | 175,694 | 0 | T | G | 21.3% | 214.0 / 18.7 | 89 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| 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 | 1462089 = | 100 (0.980) | 6 (0.060) | 5/252 | 8.3 | 5.2% | coding (1197/1206 nt) | paaJ | beta‑ketoadipyl‑CoA thiolase |
| ? | NC_000913 | 1462223 = | 128 (1.370) | coding (99/1314 nt) | paaK | phenylacetate‑CoA ligase | |||||
| * | ? | NC_000913 | 2728258 = | NA (NA) | 4 (0.040) | 4/262 | 9.1 | NA | noncoding (927/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 226685 | 36 (0.350) | 4 (0.040) | 4/262 | 9.1 | 10.5% | noncoding (927/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3410771 | 121 (1.190) | 4 (0.040) | 4/268 | 9.2 | 3.4% | coding (492/966 nt) | dusB | tRNA‑dihydrouridine synthase B |
| ? | NC_000913 | = 3410820 | 109 (1.100) | coding (541/966 nt) | dusB | tRNA‑dihydrouridine synthase B | |||||
| * | ? | NC_000913 | 250706 = | 96 (0.940) | 3 (0.030) | 3/254 | 9.6 | 2.7% | pseudogene (635/756 nt) | lafU | flagellar system protein, promoterless fragment |
| ? | NC_000913 | 250755 = | 125 (1.330) | pseudogene (684/756 nt) | lafU | flagellar system protein, promoterless fragment | |||||
| * | ? | NC_000913 | 493785 = | 88 (0.860) | 3 (0.030) | 3/262 | 9.7 | 3.3% | coding (1694/1932 nt) | dnaX | DNA polymerase III subunit tau |
| ? | NC_000913 | 493879 = | 93 (0.960) | coding (1788/1932 nt) | dnaX | DNA polymerase III subunit tau | |||||
| * | ? | NC_000913 | 2422045 = | 76 (0.750) | 3 (0.030) | 3/266 | 9.8 | 3.6% | coding (338/894 nt) | yfcH | putative NAD‑dependent epimerase YfcH |
| ? | NC_000913 | 2422157 = | 88 (0.900) | coding (450/894 nt) | yfcH | putative NAD‑dependent epimerase YfcH | |||||
| * | ? | NC_000913 | 467996 = | 90 (0.880) | 3 (0.030) | 3/264 | 9.8 | 2.8% | coding (585/819 nt) | cof | HMP‑PP phosphatase |
| ? | NC_000913 | 468078 = | 123 (1.260) | coding (667/819 nt) | cof | HMP‑PP phosphatase | |||||
| * | ? | NC_000913 | = 2833944 | 104 (1.020) | 3 (0.030) | 3/276 | 10.0 | 3.0% | coding (33/1134 nt) | norW | NADH:flavorubredoxin reductase |
| ? | NC_000913 | 2834305 = | 93 (0.910) | coding (394/1134 nt) | norW | NADH:flavorubredoxin reductase | |||||
| * | ? | NC_000913 | 2393580 = | 108 (1.060) | 3 (0.030) | 3/272 | 10.0 | 2.9% | coding (1467/1842 nt) | nuoL | NADH:quinone oxidoreductase subunit L |
| ? | NC_000913 | 2393629 = | 96 (0.960) | coding (1418/1842 nt) | nuoL | NADH:quinone oxidoreductase subunit L | |||||