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 27 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,825,061 | 0 | G | A | 38.9% | 49.7 / 17.8 | 36 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,111,747 | 0 | G | T | 33.3% | 102.6 / 27.7 | 45 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,604,344 | 0 | C | T | 32.5% | 187.9 / 64.4 | 117 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 29.3% | 98.9 / 30.0 | 58 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.7% | 295.1 / 32.2 | 146 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 75,074 | 0 | T | G | 28.6% | 100.5 / 12.4 | 49 | N136T (AAC→ACC) | thiB | thiamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.8% | 126.9 / 45.3 | 72 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,745,397 | 0 | A | C | 27.8% | 133.9 / 14.0 | 75 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 2,001,918 | 0 | A | C | 27.1% | 119.9 / 16.6 | 59 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 753,125 | 0 | T | A | 26.8% | 120.5 / 21.7 | 56 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 26.4% | 238.5 / 82.8 | 125 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,287,719 | 0 | T | A | 26.4% | 193.4 / 47.8 | 91 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 3,943,488 | 0 | T | G | 26.1% | 77.1 / 12.0 | 46 | noncoding (54/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 1,550,663 | 0 | A | C | 24.6% | 146.4 / 20.4 | 69 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 3,206,444 | 0 | T | A | 24.1% | 115.2 / 17.3 | 54 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,209,827 | 0 | T | G | 23.7% | 115.2 / 10.9 | 59 | noncoding (54/76 nt) | gltV | tRNA‑Glu |
| * | NC_000913 | 4,111,752 | 0 | T | C | 23.5% | 97.9 / 11.5 | 51 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 4,429,984 | 0 | T | G | 23.5% | 181.4 / 27.0 | 81 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 646,747 | 0 | T | G | 23.4% | 173.4 / 30.3 | 77 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 650,809 | 0 | T | G | 23.2% | 220.4 / 20.8 | 95 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| Marginal new junction evidence (lowest skew 10 of 19 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 31 (0.250) | 26/274 | 3.4 | 21.4% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1979489 | 114 (0.920) | intergenic (‑274/‑264) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 1979486 = | 114 (0.920) | 22 (0.180) | 22/274 | 4.1 | 16.2% | intergenic (‑271/‑267) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102943 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 4542690 | 88 (0.710) | 11 (0.100) | 11/256 | 6.4 | 9.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 138 (1.200) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 1979486 = | 114 (0.920) | 9 (0.070) | 9/268 | 7.3 | 7.5% | intergenic (‑271/‑267) | insA‑5/uspC | IS1 protein InsA/universal stress protein C |
| ? | NC_000913 | = 2067353 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 3 (0.040) | 3/188 | 8.4 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 4542682 = | 96 (0.780) | 6 (0.050) | 5/256 | 8.8 | 5.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 138 (1.200) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3762282 | 66 (0.530) | 4 (0.040) | 4/252 | 9.3 | 6.2% | coding (100/4134 nt) | rhsA | rhs element protein RhsA |
| ? | NC_000913 | = 3762441 | NA (NA) | coding (259/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 3970421 = | 162 (1.310) | 4 (0.030) | 4/256 | 9.4 | 2.5% | coding (289/1131 nt) | wecB | UDP‑N‑acetylglucosamine 2‑epimerase |
| ? | NC_000913 | = 3970417 | 155 (1.340) | coding (285/1131 nt) | wecB | UDP‑N‑acetylglucosamine 2‑epimerase | |||||
| * | ? | NC_000913 | = 4194972 | 96 (0.780) | 5 (0.040) | 4/272 | 9.7 | 4.9% | coding (1128/1896 nt) | thiC | phosphomethylpyrimidine synthase |
| ? | NC_000913 | 4194976 = | 99 (0.810) | coding (1124/1896 nt) | thiC | phosphomethylpyrimidine synthase | |||||
| * | ? | NC_000913 | = 3057402 | 133 (1.080) | 4 (0.030) | 4/270 | 9.7 | 3.0% | coding (1009/1233 nt) | serA | phosphoglycerate dehydrogenase |
| ? | NC_000913 | 3057406 = | 127 (1.040) | coding (1005/1233 nt) | serA | phosphoglycerate dehydrogenase | |||||