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 | 4,604,344 | 0 | C | T | 42.6% | 55.5 / 50.5 | 68 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,808,379 | 0 | C | A | 41.0% | 136.7 / 151.2 | 117 | pseudogene (64/1178 nt) | ygaY | putative transporter YgaY, N‑terminal fragment |
| * | NC_000913 | 4,111,747 | 0 | G | T | 28.9% | 105.4 / 24.5 | 45 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 28.8% | 114.0 / 24.6 | 59 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.9% | 128.0 / 36.9 | 68 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 753,125 | 0 | T | A | 27.9% | 113.8 / 23.2 | 61 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.7% | 198.8 / 11.9 | 102 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,206,435 | 0 | C | T | 27.0% | 65.0 / 16.6 | 37 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 29,496 | 0 | T | A | 26.9% | 105.1 / 22.7 | 52 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 372,640 | 0 | T | G | 23.7% | 134.2 / 11.8 | 59 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 445,558 | 0 | A | C | 23.6% | 120.6 / 21.0 | 55 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 646,747 | 0 | T | G | 23.2% | 155.9 / 26.5 | 69 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 22.9% | 100.9 / 11.0 | 48 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,745,397 | 0 | A | C | 22.7% | 132.8 / 10.7 | 67 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.8% | 193.3 / 44.3 | 87 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,068,173 | 0 | T | G | 20.8% | 185.8 / 12.1 | 77 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 888,014 | 0 | T | G | 20.5% | 174.6 / 11.8 | 73 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 2,667,126 | 0 | A | C | 20.3% | 160.6 / 10.7 | 69 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 95 (0.930) | 16 (0.170) | 16/258 | 4.5 | 16.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 79 (0.830) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 92 (0.900) | 10 (0.110) | 9/258 | 6.6 | 10.8% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 79 (0.830) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 697048 = | 112 (1.100) | 3 (0.030) | 3/252 | 9.5 | 2.7% | intergenic (‑1/+9) | leuW/metT | tRNA‑Leu/tRNA‑Met |
| ? | NC_000913 | 697144 = | 113 (1.220) | intergenic (‑11/+369) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 596972 | 124 (1.220) | 3 (0.030) | 3/252 | 9.5 | 2.4% | coding (1373/1374 nt) | cusC | copper/silver export system outer membrane channel |
| ? | NC_000913 | = 3522640 | 131 (1.410) | coding (112/780 nt) | hofM | DNA utilization protein HofM | |||||
| * | ? | NC_000913 | 1172593 = | 89 (0.870) | 3 (0.030) | 3/262 | 9.7 | 3.5% | coding (1372/3447 nt) | mfd | transcription‑repair coupling factor |
| ? | NC_000913 | = 1172589 | 83 (0.860) | coding (1376/3447 nt) | mfd | transcription‑repair coupling factor | |||||
| * | ? | NC_000913 | 3501845 = | 103 (1.010) | 3 (0.030) | 3/274 | 9.9 | 2.9% | coding (578/1023 nt) | frlB | fructoselysine 6‑phosphate deglycase |
| ? | NC_000913 | = 3503273 | 98 (0.970) | coding (107/786 nt) | frlD | fructoselysine 6‑kinase | |||||
| * | ? | NC_000913 | 1906642 = | 114 (1.120) | 3 (0.030) | 3/270 | 9.9 | 2.5% | coding (419/810 nt) | rlmA | 23S rRNA m(1)G745 methyltransferase |
| ? | NC_000913 | 1906718 = | 122 (1.220) | coding (343/810 nt) | rlmA | 23S rRNA m(1)G745 methyltransferase | |||||
| * | ? | NC_000913 | 696664 = | 102 (1.000) | 3 (0.030) | 3/270 | 9.9 | 2.7% | noncoding (77/77 nt) | metU | tRNA‑Met |
| ? | NC_000913 | 697135 = | 118 (1.180) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 4498315 | 4 (0.040) | 3 (0.030) | 3/276 | 10.0 | 42.9% | noncoding (135/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 4498319 = | NA (NA) | noncoding (139/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 3186230 | 5 (0.050) | 3 (0.030) | 3/276 | 10.0 | 37.5% | noncoding (135/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 3186234 = | NA (NA) | noncoding (139/1331 nt) | IS2 | repeat region | |||||