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 | 4,027,436 | 0 | T | G | 59.1% | 22.8 / 21.4 | 22 | intergenic (+208/+173) | fre/fadA | flavin reductase/3‑ketoacyl‑CoA thiolase |
| * | NC_000913 | 650,809 | 0 | T | G | 37.0% | 71.6 / 23.0 | 54 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 36.1% | 41.0 / 27.2 | 36 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 3,206,444 | 0 | T | A | 34.3% | 46.5 / 20.7 | 35 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 33.3% | 55.3 / 12.5 | 30 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 32.8% | 103.0 / 33.4 | 65 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 29.0% | 48.8 / 11.5 | 31 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.0% | 142.4 / 10.5 | 75 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 802,118 | 0 | A | C | 26.1% | 86.5 / 11.0 | 46 | T78P (ACC→CCC) | ybhI | putative tricarboxylate transporter |
| * | NC_000913 | 445,558 | 0 | A | C | 23.8% | 76.3 / 16.4 | 42 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 29,496 | 0 | T | A | 23.1% | 96.4 / 13.1 | 39 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 646,747 | 0 | T | G | 23.1% | 106.1 / 17.3 | 52 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 646,760 | 0 | T | C | 22.4% | 103.4 / 13.9 | 49 | K250K (AAA→AAG) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 2,168,966 | 0 | A | C | 21.9% | 139.2 / 11.6 | 64 | I85I (ATA→ATC) | yegS | lipid kinase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 21.6% | 107.5 / 16.7 | 51 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 21.4% | 205.6 / 20.5 | 98 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.1% | 177.0 / 36.9 | 76 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| 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 | 4542682 = | 68 (1.060) | 10 (0.170) | 9/258 | 3.6 | 14.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 57 (0.950) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 555833 | 77 (1.200) | 4 (0.070) | 4/244 | 5.1 | 5.1% | coding (1223/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 556784 | 82 (1.450) | coding (90/213 nt) | ybcJ | putative RNA‑binding protein YbcJ | |||||
| * | ? | NC_000913 | 161693 = | 45 (0.700) | 3 (0.050) | 3/252 | 5.7 | 6.1% | coding (339/531 nt) | thpR | RNA 2',3'‑cyclic phosphodiesterase |
| ? | NC_000913 | 163801 = | 51 (0.870) | coding (1697/2430 nt) | hrpB | putative ATP‑dependent RNA helicase HrpB | |||||
| * | ? | NC_000913 | 4215494 = | 59 (0.920) | 3 (0.050) | 3/262 | 5.9 | 5.0% | coding (17/1602 nt) | aceB | malate synthase A |
| ? | NC_000913 | = 4215490 | 57 (0.940) | coding (13/1602 nt) | aceB | malate synthase A | |||||
| * | ? | NC_000913 | = 4511620 | 42 (0.660) | 3 (0.050) | 3/276 | 6.1 | 7.4% | coding (795/957 nt) | fecD | ferric citrate ABC transporter membrane subunit FecD |
| ? | NC_000913 | = 4511656 | 33 (0.520) | coding (759/957 nt) | fecD | ferric citrate ABC transporter membrane subunit FecD | |||||