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 | 3,206,435 | 0 | C | T | 32.3% | 40.5 / 18.3 | 31 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 31.6% | 148.0 / 27.9 | 57 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 445,558 | 0 | A | C | 30.6% | 71.7 / 26.7 | 49 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 4,568,504 | 0 | T | G | 30.3% | 133.4 / 13.8 | 76 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,001,918 | 0 | A | C | 30.0% | 86.9 / 15.7 | 50 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,745,397 | 0 | A | C | 29.7% | 115.1 / 16.9 | 75 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| * | NC_000913 | 650,809 | 0 | T | G | 29.0% | 110.8 / 20.5 | 62 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,556,207 | 0 | T | C | 28.6% | 71.9 / 13.8 | 42 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 4,296,060 | 0 | C | T | 25.9% | 163.8 / 51.7 | 81 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.5% | 85.5 / 21.7 | 47 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 888,014 | 0 | T | G | 25.0% | 115.7 / 23.3 | 64 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,604,344 | 0 | C | T | 24.4% | 90.7 / 12.6 | 45 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,645,034 | 0 | A | C | 23.6% | 111.9 / 13.6 | 55 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 433,634 | 0 | T | G | 22.7% | 191.5 / 11.2 | 97 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| * | NC_000913 | 3,740,909 | 0 | T | G | 22.2% | 128.9 / 19.3 | 63 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 4,111,752 | 0 | T | C | 22.2% | 128.0 / 10.2 | 63 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 29,496 | 0 | T | A | 21.4% | 108.1 / 13.2 | 42 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 372,640 | 0 | T | G | 21.2% | 137.0 / 18.3 | 66 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 332,991 | 0 | G | T | 20.7% | 165.4 / 15.8 | 58 | L207F (TTG→TTT) | pdeL | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 4,568,512 | 0 | C | A | 20.4% | 164.3 / 14.5 | 54 | R3L (CGT→CTT) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 50 (0.560) | 7 (0.080) | 7/256 | 5.8 | 9.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 88 (1.060) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 55 (0.620) | 7 (0.080) | 6/256 | 6.2 | 9.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 89 (1.070) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 2001124 = | 154 (1.730) | 4 (0.050) | 4/262 | 7.2 | 2.6% | coding (666/720 nt) | fliA | RNA polymerase, sigma 28 (sigma F) factor |
| ? | NC_000913 | = 2001119 | 149 (1.750) | coding (671/720 nt) | fliA | RNA polymerase, sigma 28 (sigma F) factor | |||||
| * | ? | NC_000913 | 3484544 = | 119 (1.330) | 3 (0.040) | 3/254 | 7.6 | 2.6% | coding (55/870 nt) | prkB | putative phosphoribulokinase |
| ? | NC_000913 | = 3484540 | 112 (1.360) | coding (51/870 nt) | prkB | putative phosphoribulokinase | |||||
| * | ? | NC_000913 | = 3827490 | 67 (0.750) | 4 (0.050) | 3/270 | 7.9 | 5.9% | coding (1176/1206 nt) | gltS | glutamate:sodium symporter |
| ? | NC_000913 | 3827494 = | 62 (0.710) | coding (1172/1206 nt) | gltS | glutamate:sodium symporter | |||||
| * | ? | NC_000913 | = 2135397 | 77 (0.860) | 3 (0.030) | 3/270 | 7.9 | 3.8% | coding (256/2163 nt) | wzc | protein‑tyrosine kinase Wzc |
| ? | NC_000913 | 2135402 = | 74 (0.840) | coding (251/2163 nt) | wzc | protein‑tyrosine kinase Wzc | |||||
| * | ? | NC_000913 | = 555279 | 99 (1.110) | 3 (0.030) | 3/272 | 7.9 | 2.9% | coding (669/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | 555283 = | 100 (1.130) | coding (673/1386 nt) | cysS | cysteine‑‑tRNA ligase | |||||