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 30 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 | 43.8% | 111.3 / 92.9 | 128 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 770,897 | 0 | T | G | 41.0% | 30.7 / 17.7 | 39 | intergenic (+286/‑561) | mngB/cydA | alpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I |
| * | NC_000913 | 3,556,207 | 0 | T | C | 36.2% | 60.4 / 17.1 | 47 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 29,496 | 0 | T | A | 32.7% | 96.6 / 29.1 | 55 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,775,467 | 0 | A | C | 29.2% | 139.0 / 12.4 | 72 | intergenic (+23/‑120) | aroD/ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 28.0% | 92.1 / 17.8 | 50 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 501,575 | 0 | A | C | 26.8% | 116.5 / 13.5 | 56 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,667,126 | 0 | A | C | 26.5% | 199.2 / 25.6 | 98 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 3,404,218 | 0 | T | G | 25.6% | 182.5 / 31.2 | 86 | G245G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.5% | 226.4 / 39.9 | 106 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 501,572 | 0 | A | C | 25.4% | 120.3 / 10.4 | 55 | V556G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 2,001,918 | 0 | A | C | 25.4% | 250.2 / 32.6 | 110 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 599,576 | 0 | T | G | 25.4% | 123.6 / 22.9 | 59 | V288G (GTG→GGG) | cusA | copper/silver export system RND permease |
| * | NC_000913 | 501,564 | 0 | A | C | 25.0% | 132.5 / 19.4 | 60 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 372,640 | 0 | T | G | 24.7% | 197.2 / 15.7 | 89 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 650,809 | 0 | T | G | 24.5% | 201.3 / 25.6 | 94 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,782,509 | 0 | A | C | 24.5% | 391.9 / 32.8 | 186 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 888,014 | 0 | T | G | 24.3% | 236.9 / 18.0 | 103 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 3,401,459 | 0 | T | C | 23.6% | 209.7 / 24.7 | 106 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,568,504 | 0 | T | G | 23.4% | 310.6 / 15.1 | 138 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| Marginal new junction evidence (lowest skew 10 of 16 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 96 (0.800) | 15 (0.130) | 15/260 | 5.7 | 12.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 119 (1.060) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 110 (0.910) | 18 (0.160) | 15/260 | 5.7 | 13.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 120 (1.060) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 2817942 | 146 (1.210) | 9 (0.090) | 7/238 | 8.1 | 7.4% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818078 = | 102 (0.990) | noncoding (58/77 nt) | argZ | tRNA‑Arg | |||||
| * | ? | NC_000913 | 2817783 = | 136 (1.130) | 6 (0.060) | 5/238 | 9.1 | 5.0% | intergenic (‑280/+1) | yqaB/argQ | fructose‑1‑phosphatase/tRNA‑Arg |
| ? | NC_000913 | = 2817922 | 113 (1.100) | intergenic (‑62/+137) | argQ/argZ | tRNA‑Arg/tRNA‑Arg | |||||
| * | ? | NC_000913 | = 1979489 | 126 (1.040) | 18 (0.150) | 7/278 | 9.1 | 12.5% | intergenic (‑274/‑264) | 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 = | 98 (0.810) | 3 (0.030) | 3/254 | 10.9 | 3.2% | coding (486/1350 nt) | accC | biotin carboxylase |
| ? | NC_000913 | = 3406398 | 93 (0.840) | coding (482/1350 nt) | accC | biotin carboxylase | |||||
| * | ? | NC_000913 | 1722616 = | 108 (0.900) | 3 (0.030) | 3/256 | 10.9 | 2.9% | coding (496/2013 nt) | ydhK | putative transporter YdhK |
| ? | NC_000913 | = 1722612 | 102 (0.920) | coding (492/2013 nt) | ydhK | putative transporter YdhK | |||||
| * | ? | NC_000913 | = 3000956 | 123 (1.020) | 3 (0.030) | 3/266 | 11.2 | 2.7% | coding (612/2259 nt) | xdhA | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| ? | NC_000913 | = 3000997 | 99 (0.860) | coding (653/2259 nt) | xdhA | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA | |||||
| * | ? | NC_000913 | = 3170367 | 104 (0.860) | 3 (0.030) | 3/274 | 11.3 | 2.9% | coding (540/660 nt) | qseB | DNA‑binding transcriptional activator QseB |
| ? | NC_000913 | = 3171379 | 100 (0.840) | coding (896/1350 nt) | qseC | sensory histidine kinase QseC | |||||
| * | ? | NC_000913 | = 2739278 | 113 (0.940) | 3 (0.030) | 3/270 | 11.3 | 3.0% | coding (792/1122 nt) | tyrA | fused chorismate mutase/prephenate dehydrogenase |
| ? | NC_000913 | 2739720 = | 85 (0.730) | coding (350/1122 nt) | tyrA | fused chorismate mutase/prephenate dehydrogenase | |||||