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 21 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 | 44.2% | 70.0 / 53.8 | 77 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 33.3% | 157.0 / 37.9 | 93 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 29,496 | 0 | T | A | 32.6% | 79.0 / 21.4 | 46 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 1,825,061 | 0 | G | A | 31.1% | 75.0 / 15.7 | 45 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.1% | 266.9 / 18.3 | 140 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,111,747 | 0 | G | T | 27.3% | 140.3 / 23.8 | 55 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,168,966 | 0 | A | C | 26.3% | 197.8 / 17.0 | 95 | I85I (ATA→ATC) | yegS | lipid kinase |
| * | NC_000913 | 650,809 | 0 | T | G | 26.2% | 151.0 / 20.4 | 80 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 26.2% | 113.6 / 24.1 | 61 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,782,509 | 0 | A | C | 25.9% | 254.0 / 25.4 | 141 | V73G (GTA→GGA) | ypjA | adhesin‑like autotransporter YpjA |
| * | NC_000913 | 888,014 | 0 | T | G | 24.4% | 177.3 / 19.7 | 86 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 372,640 | 0 | T | G | 23.4% | 158.7 / 14.4 | 77 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 501,575 | 0 | A | C | 22.7% | 91.9 / 11.9 | 44 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 836,756 | 0 | T | G | 22.5% | 149.7 / 12.2 | 71 | F136V (TTT→GTT) | hcxB | hydroxycarboxylate dehydrogenase B |
| * | NC_000913 | 4,223,593 | 0 | T | G | 22.1% | 222.1 / 10.4 | 95 | K12N (AAA→AAC) | iclR | DNA‑binding transcriptional repressor IclR |
| * | NC_000913 | 4,429,984 | 0 | T | G | 21.9% | 156.3 / 25.6 | 73 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 753,125 | 0 | T | A | 21.8% | 217.0 / 21.1 | 87 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 445,558 | 0 | A | C | 21.4% | 87.7 / 11.1 | 42 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 501,564 | 0 | A | C | 21.1% | 117.6 / 11.9 | 52 | *559E (TAA→GAA) | ybaL | putative transporter YbaL |
| * | NC_000913 | 1,489,174 | 0 | G | T | 20.6% | 190.1 / 13.7 | 68 | G315C (GGT→TGT) | aldA | aldehyde dehydrogenase A |
| Marginal new junction evidence (lowest skew 10 of 24 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 76 (0.670) | 16 (0.150) | 15/260 | 4.9 | 15.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 98 (0.920) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 86 (0.760) | 15 (0.140) | 12/260 | 5.7 | 14.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 100 (0.940) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 3 (0.030) | 3/226 | 8.9 | 2.6% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 111 (1.200) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 3260736 = | 118 (1.040) | 4 (0.040) | 4/268 | 9.2 | 3.6% | coding (1683/2295 nt) | tdcE | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 |
| ? | NC_000913 | = 3260972 | 99 (0.900) | coding (1447/2295 nt) | tdcE | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4 | |||||
| * | ? | NC_000913 | = 3844897 | 165 (1.450) | 4 (0.040) | 4/274 | 9.4 | 2.4% | coding (934/1767 nt) | adeD | adenine deaminase |
| ? | NC_000913 | 3844901 = | 161 (1.440) | coding (938/1767 nt) | adeD | adenine deaminase | |||||
| * | ? | NC_000913 | 1272758 = | 138 (1.220) | 3 (0.030) | 3/256 | 9.6 | 2.8% | coding (252/696 nt) | chaC | glutathione‑specific gamma‑glutamylcyclotransferase |
| ? | NC_000913 | 1273352 = | 85 (0.810) | coding (248/354 nt) | ychN | DsrE/F sulfur relay family protein YchN | |||||
| * | ? | NC_000913 | 1516329 = | 116 (1.020) | 3 (0.030) | 3/258 | 9.7 | 2.9% | coding (752/1425 nt) | patD | gamma‑aminobutyraldehyde dehydrogenase |
| ? | NC_000913 | 1516626 = | 95 (0.900) | coding (1049/1425 nt) | patD | gamma‑aminobutyraldehyde dehydrogenase | |||||
| * | ? | NC_000913 | = 3923338 | 133 (1.170) | 3 (0.030) | 3/262 | 9.8 | 1.9% | coding (343/624 nt) | rsmG | 16S rRNA m(7)G527 methyltransferase |
| ? | NC_000913 | = 3923515 | 179 (1.670) | coding (166/624 nt) | rsmG | 16S rRNA m(7)G527 methyltransferase | |||||
| * | ? | NC_000913 | 224910 = | NA (NA) | 3 (0.030) | 3/262 | 9.8 | NA | noncoding (1140/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | 225157 = | NA (NA) | noncoding (1387/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | 3410758 = | 154 (1.360) | 3 (0.030) | 3/268 | 9.9 | 2.3% | coding (479/966 nt) | dusB | tRNA‑dihydrouridine synthase B |
| ? | NC_000913 | 3410835 = | 112 (1.020) | coding (556/966 nt) | dusB | tRNA‑dihydrouridine synthase B | |||||