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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,111,747 | 0 | G | T | 45.0% | 15.5 / 20.1 | 20 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 445,558 | 0 | A | C | 39.1% | 25.2 / 13.2 | 23 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,028,736 | 0 | G | T | 34.5% | 88.0 / 56.1 | 55 | P13T (CCG→ACG) | fadA | 3‑ketoacyl‑CoA thiolase |
| * | NC_000913 | 4,604,344 | 0 | C | T | 34.2% | 55.5 / 18.8 | 41 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 32.1% | 40.7 / 17.4 | 28 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,531,440 | 0 | A | C | 30.2% | 83.9 / 14.1 | 44 | Y334D (TAT→GAT) | yhgE | putative transport protein YhgE |
| * | NC_000913 | 374,972 | 0 | T | C | 29.2% | 140.3 / 85.2 | 106 | intergenic (+91/‑487) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 374,986 | 0 | T | C | 28.8% | 139.8 / 82.6 | 104 | intergenic (+105/‑473) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| * | NC_000913 | 753,125 | 0 | T | A | 27.9% | 84.3 / 16.6 | 43 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,347,284 | 0 | T | G | 27.8% | 47.0 / 34.9 | 37 | intergenic (+134/‑100) | nrdA/nrdB | ribonucleoside‑diphosphate reductase 1 subunit alpha/ribonucleoside‑diphosphate reductase 1 subunit beta |
| * | NC_000913 | 2,347,287 | 1 | . | G | 27.3% | 47.3 / 39.5 | 33 | intergenic (+137/‑97) | nrdA/nrdB | ribonucleoside‑diphosphate reductase 1 subunit alpha/ribonucleoside‑diphosphate reductase 1 subunit beta |
| * | NC_000913 | 2,347,287 | 2 | . | A | 27.3% | 41.0 / 40.8 | 33 | intergenic (+137/‑97) | nrdA/nrdB | ribonucleoside‑diphosphate reductase 1 subunit alpha/ribonucleoside‑diphosphate reductase 1 subunit beta |
| * | NC_000913 | 4,568,512 | 0 | C | A | 25.6% | 97.0 / 14.8 | 39 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,068,173 | 0 | T | G | 23.2% | 134.5 / 13.7 | 56 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 3,926,366 | 0 | A | C | 22.9% | 110.7 / 13.0 | 48 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 29,496 | 0 | T | A | 22.5% | 92.9 / 12.0 | 40 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,296,060 | 0 | C | T | 22.5% | 73.9 / 17.7 | 40 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 377321 = | NA (NA) | 17 (0.340) | 8/266 | 3.3 | 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 | |||||
| * | ? | NC_000913 | = 25796 | NA (NA) | 17 (0.330) | 8/272 | 3.4 | NA | noncoding (1/34 nt) | other | REP2b |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 6 (0.130) +GAACGCCTTATCCGGT |
6/242 | 3.6 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 9 (0.180) +T |
7/272 | 3.6 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 3814351 = | 63 (1.220) | 6 (0.130) | 5/248 | 4.0 | 8.7% | coding (420/456 nt) | dut | deoxyuridine triphosphatase |
| ? | NC_000913 | 3815455 = | 69 (1.480) | coding (314/642 nt) | pyrE | orotate phosphoribosyltransferase | |||||
| * | ? | NC_000913 | 3736206 = | NA (NA) | 4 (0.100) | 3/210 | 4.3 | NA | noncoding (2/34 nt) | other | REP268b |
| ? | NC_000913 | 4484415 = | NA (NA) | noncoding (3/34 nt) | other | REP342b | |||||
| * | ? | NC_000913 | = 2518224 | 60 (1.170) | 6 (0.130) | 4/238 | 4.3 | 12.1% | noncoding (8/76 nt) | alaW | tRNA‑Ala |
| ? | NC_000913 | = 2521057 | 35 (0.780) | noncoding (7/76 nt) | valX | tRNA‑Val | |||||
| * | ? | NC_000913 | = 4542690 | 33 (0.640) | 4 (0.080) | 4/256 | 4.5 | 7.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 66 (1.370) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1966882 = | 51 (0.990) | 4 (0.080) | 4/252 | 4.5 | 7.3% | coding (156/645 nt) | cheZ | chemotaxis protein CheZ |
| ? | NC_000913 | 1966984 = | 55 (1.160) | coding (54/645 nt) | cheZ | chemotaxis protein CheZ | |||||
| * | ? | NC_000913 | = 3255253 | NA (NA) | 4 (0.090) | 3/228 | 4.6 | NA | intergenic (+46/+88) | yhaL/cyuA | uncharacterized protein YhaL/putative L‑cysteine desulfidase CyuA |
| ? | NC_000913 | = 3741024 | NA (NA) | intergenic (+66/+85) | avtA/ysaA | valine‑‑pyruvate aminotransferase/putative electron transport protein YsaA | |||||