mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 43.2% | 101.8 / 69.4 | 95 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 34.2% | 52.9 / 21.1 | 38 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 32.5% | 60.5 / 14.8 | 40 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,740,909 | 0 | T | G | 31.4% | 150.0 / 32.5 | 86 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 501,575 | 0 | A | C | 31.2% | 86.3 / 16.6 | 48 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 4,568,504 | 0 | T | G | 31.2% | 168.3 / 14.8 | 94 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 30.2% | 130.2 / 33.1 | 53 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 30.0% | 146.7 / 63.1 | 91 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 501,564 | 0 | A | C | 29.8% | 74.3 / 29.4 | 47 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 1,825,061 | 0 | G | A | 28.2% | 76.2 / 13.8 | 39 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.1% | 110.2 / 21.5 | 57 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,429,984 | 0 | T | G | 27.4% | 142.7 / 29.9 | 73 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 445,558 | 0 | A | C | 25.5% | 96.7 / 16.9 | 47 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,628,649 | 0 | A | C | 25.0% | 136.0 / 15.2 | 64 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 3,206,435 | 0 | C | T | 24.4% | 89.3 / 13.9 | 41 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,401,459 | 0 | T | C | 24.1% | 177.3 / 21.9 | 87 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,296,060 | 0 | C | T | 24.0% | 203.5 / 62.4 | 104 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 29,496 | 0 | T | A | 23.7% | 142.9 / 26.3 | 59 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 175,694 | 0 | T | G | 23.5% | 178.5 / 15.7 | 81 | G196G (GGT→GGG) | clcA | chloride:H(+) antiporter ClcA |
| * | NC_000913 | 3,745,397 | 0 | A | C | 23.2% | 152.5 / 13.9 | 82 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 79 (0.740) | 5 (0.050) | 5/258 | 8.2 | 6.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 73 (0.730) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1287548 | 68 (0.640) | 4 (0.040) | 3/258 | 9.4 | 4.9% | noncoding (75/85 nt) | tyrT | tRNA‑Tyr |
| ? | NC_000913 | = 1287615 | 93 (0.930) | noncoding (8/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 1287329 | 62 (0.580) | 4 (0.040) | 3/260 | 9.4 | 6.2% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | = 1287540 | 62 (0.620) | noncoding (83/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | 2728258 = | NA (NA) | 3 (0.030) | 3/262 | 9.5 | NA | noncoding (927/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 2525083 | 111 (1.040) | 3 (0.030) | 3/264 | 9.5 | 2.4% | intergenic (‑205/‑44) | xapA/yfeN | xanthosine phosphorylase/conserved outer membrane protein YfeN |
| ? | NC_000913 | = 2526021 | 140 (1.370) | coding (836/927 nt) | yfeR | putative LysR‑type DNA‑binding transcriptional regulator YfeR | |||||
| * | ? | NC_000913 | = 226685 | 43 (0.400) | 3 (0.030) | 3/262 | 9.5 | 6.8% | noncoding (927/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 3616309 = | 112 (1.050) | 3 (0.030) | 3/268 | 9.6 | 3.4% | coding (128/834 nt) | nikC | Ni(2(+)) ABC transporter membrane subunit NikC |
| ? | NC_000913 | = 3618249 | 63 (0.610) | coding (474/807 nt) | nikE | Ni(2(+)) ABC transporter ATP binding subunit NikE | |||||
| * | ? | NC_000913 | = 2154459 | 67 (0.630) | 3 (0.030) | 3/268 | 9.6 | 3.6% | coding (444/1248 nt) | mdtA | multidrug efflux pump membrane fusion protein MdtA |
| ? | NC_000913 | 2154736 = | 96 (0.930) | coding (721/1248 nt) | mdtA | multidrug efflux pump membrane fusion protein MdtA | |||||
| * | ? | NC_000913 | = 276363 | 125 (1.170) | 3 (0.030) | 3/268 | 9.6 | 2.5% | coding (1039/1404 nt) | mmuP | S‑methyl‑L‑methionine transporter |
| ? | NC_000913 | 276367 = | 113 (1.090) | coding (1043/1404 nt) | mmuP | S‑methyl‑L‑methionine transporter | |||||
| * | ? | NC_000913 | = 274767 | NA (NA) | 3 (0.030) | 3/270 | 9.6 | NA | noncoding (383/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274771 = | NA (NA) | noncoding (379/1195 nt) | IS5 | repeat region | |||||