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 28 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,443,929 | 0 | T | C | 41.9% | 49.1 / 110.8 | 93 | M81V (ATG→GTG) | yfcL | protein YfcL |
| * | NC_000913 | 4,604,344 | 0 | C | T | 38.2% | 106.4 / 50.3 | 89 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,037,496 | 0 | A | T | 36.1% | 122.4 / 96.2 | 83 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 372,640 | 0 | T | G | 35.4% | 69.0 / 20.4 | 49 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 1,270,009 | 0 | T | A | 35.2% | 107.2 / 100.1 | 93 | intergenic (+86/+229) | rdlB/ldrC | small regulatory antisense RNA RdlB/small toxic polypeptide LdrC |
| * | NC_000913 | 3,206,435 | 0 | C | T | 33.9% | 68.0 / 33.4 | 56 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.1% | 111.1 / 22.4 | 61 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 753,125 | 0 | T | A | 29.7% | 132.2 / 26.7 | 64 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.6% | 217.9 / 15.0 | 109 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,622,761 | 0 | G | C | 29.6% | 346.2 / 208.9 | 203 | R1190R (CGG→CGC) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 1,825,061 | 0 | G | A | 29.3% | 69.2 / 11.4 | 41 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,296,060 | 0 | C | T | 29.1% | 161.7 / 77.8 | 103 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 650,809 | 0 | T | G | 27.7% | 170.5 / 19.2 | 83 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 888,014 | 0 | T | G | 27.7% | 135.8 / 15.1 | 65 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,161,148 | 0 | G | A | 27.3% | 167.2 / 23.2 | 88 | E28K (GAA→AAA) | fabR | DNA‑binding transcriptional repressor FabR |
| * | NC_000913 | 29,496 | 0 | T | A | 26.7% | 177.8 / 29.8 | 75 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,111,747 | 0 | G | T | 26.4% | 186.6 / 27.8 | 72 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,326,450 | 0 | T | G | 26.3% | 156.8 / 33.2 | 76 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,206,444 | 0 | T | A | 25.0% | 102.1 / 13.6 | 52 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 4,111,752 | 0 | T | C | 24.4% | 180.0 / 10.5 | 82 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| 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 | 1207790 = | 126 (1.290) | 21 (0.240) | 19/242 | 3.0 | 16.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 99 (1.150) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 4542690 | 92 (0.940) | 16 (0.180) | 15/256 | 4.0 | 15.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 93 (1.020) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1207805 | 108 (1.100) | 7 (0.080) | 7/242 | 6.1 | 6.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 98 (1.130) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1722616 = | 94 (0.960) | 3 (0.030) | 3/252 | 8.3 | 3.3% | coding (496/2013 nt) | ydhK | putative transporter YdhK |
| ? | NC_000913 | = 1722612 | 87 (0.970) | coding (492/2013 nt) | ydhK | putative transporter YdhK | |||||
| * | ? | NC_000913 | 1287460 = | 73 (0.750) | 5 (0.060) | 3/254 | 8.3 | 5.6% | intergenic (‑132/+78) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287568 = | 102 (1.130) | noncoding (55/85 nt) | tyrT | tRNA‑Tyr | |||||