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 27 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 | 42.7% | 95.0 / 76.5 | 96 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 33.3% | 55.5 / 25.6 | 42 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 33.1% | 213.1 / 19.7 | 119 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,556,205 | 0 | A | C | 30.0% | 118.1 / 16.2 | 60 | S215R (AGT→AGG) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 29.3% | 156.9 / 28.8 | 82 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,556,207 | 0 | T | C | 28.3% | 108.6 / 21.0 | 60 | S215G (AGT→GGT) ‡ | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 3,745,397 | 0 | A | C | 27.9% | 114.1 / 16.2 | 68 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 372,640 | 0 | T | G | 27.4% | 119.5 / 14.0 | 62 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 501,575 | 0 | A | C | 26.1% | 92.2 / 16.6 | 46 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 753,125 | 0 | T | A | 26.1% | 96.5 / 13.7 | 46 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.7% | 201.1 / 63.2 | 101 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,068,173 | 0 | T | G | 24.6% | 148.4 / 16.3 | 69 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| * | NC_000913 | 4,111,747 | 0 | G | T | 24.4% | 128.5 / 20.9 | 45 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,608,244 | 0 | T | G | 24.4% | 144.1 / 10.1 | 82 | V443G (GTG→GGG) | hyfF | hydrogenase 4 component F |
| * | NC_000913 | 29,496 | 0 | T | A | 24.1% | 130.4 / 21.6 | 54 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 753,114 | 0 | G | T | 24.0% | 137.3 / 10.9 | 50 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,111,752 | 0 | T | C | 23.7% | 118.2 / 10.6 | 59 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.3% | 152.1 / 31.6 | 73 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 23.0% | 193.6 / 26.6 | 87 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,275,611 | 0 | A | C | 22.5% | 157.1 / 16.1 | 71 | E110D (GAA→GAC) | garD | galactarate dehydratase |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 103 (0.890) | 15 (0.140) | 12/258 | 5.5 | 14.0% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 88 (0.820) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 114 (0.990) | 12 (0.110) | 10/258 | 6.2 | 10.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 89 (0.830) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979643 = | 86 (0.750) | 25 (0.220) | 7/276 | 7.6 | 22.5% | intergenic (‑428/‑110) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3722996 | 125 (1.090) | 6 (0.050) | 6/272 | 8.0 | 4.6% | coding (1402/2070 nt) | glyS | glycine‑‑tRNA ligase subunit beta |
| ? | NC_000913 | 3723025 = | 125 (1.100) | coding (1373/2070 nt) | glyS | glycine‑‑tRNA ligase subunit beta | |||||
| * | ? | NC_000913 | = 1979646 | 86 (0.750) | 22 (0.190) | 6/276 | 8.0 | 20.4% | intergenic (‑431/‑107) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 3406402 = | 105 (0.910) | 3 (0.030) | 3/252 | 9.2 | 3.0% | coding (486/1350 nt) | accC | biotin carboxylase |
| ? | NC_000913 | = 3406398 | 99 (0.940) | coding (482/1350 nt) | accC | biotin carboxylase | |||||
| * | ? | NC_000913 | = 940590 | 141 (1.280) | 9 (0.080) +GAACG |
3/254 | 9.2 | 6.0% | coding (1163/1293 nt) | serS | serine‑‑tRNA ligase |
| ? | NC_000913 | 940591 = | 143 (1.240) | coding (1164/1293 nt) | serS | serine‑‑tRNA ligase | |||||
| * | ? | NC_000913 | = 4163131 | 172 (1.520) | 4 (0.040) +GCT |
3/266 | 9.5 | 2.3% | coding (140/1101 nt) | trmA | tRNA m(5)U54 methyltransferase |
| ? | NC_000913 | 4163132 = | 172 (1.490) | coding (139/1101 nt) | trmA | tRNA m(5)U54 methyltransferase | |||||
| * | ? | NC_000913 | = 3195519 | 121 (1.050) | 3 (0.030) | 3/276 | 9.6 | 2.3% | coding (1235/1434 nt) | rfaE | fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase |
| ? | NC_000913 | = 3195588 | 138 (1.200) | coding (1166/1434 nt) | rfaE | fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase | |||||
| * | ? | NC_000913 | = 2505678 | 93 (0.810) | 3 (0.030) | 3/272 | 9.6 | 3.1% | coding (955/1086 nt) | ypdF | aminopeptidase |
| ? | NC_000913 | 2505683 = | 95 (0.840) | coding (950/1086 nt) | ypdF | aminopeptidase | |||||