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 29 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,465,044 | 0 | C | T | 71.7% | 162.6 / 75.4 | 106 | P375S (CCG→TCG) | gspL | Type II secretion system protein GspL |
| * | NC_000913 | 3,931,176 | 1 | . | G | 69.2% | 178.6 / 84.2 | 78 | intergenic (‑83/‑140) | ravA/kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| * | NC_000913 | 689,995 | 0 | A | G | 68.3% | 96.9 / 63.5 | 79 | V296A (GTA→GCA) | lnt | apolipoprotein N‑acyltransferase |
| * | NC_000913 | 2,539,043 | 0 | C | T | 65.1% | 88.8 / 68.7 | 84 | G181S (GGC→AGC) | cysM | cysteine synthase B |
| * | NC_000913 | 4,492,578 | 0 | G | . | 62.5% | 29.1 / 82.9 | 48 | intergenic (‑53/+9) | idnT/idnO | L‑idonate/5‑ketogluconate/gluconate transporter/5‑keto‑D‑gluconate 5‑reductase |
| * | NC_000913 | 1,931,192 | 0 | C | T | 56.4% | 37.9 / 124.1 | 101 | C104C (TGC→TGT) | purT | phosphoribosylglycinamide formyltransferase 2 |
| * | NC_000913 | 1,269,726 | 0 | C | T | 45.0% | 73.6 / 122.8 | 100 | G29S (GGC→AGC) | ldrB | small toxic polypeptide LdrB |
| * | NC_000913 | 4,604,344 | 0 | C | T | 44.6% | 37.0 / 39.6 | 56 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 37.2% | 83.2 / 24.3 | 43 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,556,205 | 0 | A | C | 35.3% | 46.8 / 11.9 | 34 | S215R (AGT→AGG) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 1,269,897 | 0 | T | G | 34.4% | 147.6 / 167.7 | 122 | noncoding (40/66 nt) | rdlB | small regulatory antisense RNA RdlB |
| * | NC_000913 | 29,496 | 0 | T | A | 34.2% | 74.5 / 19.9 | 41 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 2,667,126 | 0 | A | C | 33.3% | 77.4 / 16.1 | 54 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 4,111,752 | 0 | T | C | 33.3% | 71.9 / 10.8 | 48 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 753,125 | 0 | T | A | 30.4% | 113.4 / 25.8 | 56 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.0% | 51.6 / 17.5 | 40 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 29.8% | 92.2 / 27.6 | 57 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 29.2% | 111.1 / 27.2 | 66 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 650,809 | 0 | T | G | 28.6% | 101.1 / 12.4 | 56 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,140,926 | 0 | A | C | 27.9% | 114.5 / 13.0 | 61 | G229G (GGT→GGG) | asmA | putative assembly protein AsmA |
| 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 | 57 (0.660) | 6 (0.070) | 6/256 | 6.2 | 7.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 87 (1.070) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 5 (0.080) | 3/200 | 6.6 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 3045997 | 70 (0.810) | 7 (0.090) | 4/254 | 7.0 | 11.1% | intergenic (‑96/+171) | ygfF/gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase |
| ? | NC_000913 | = 3046078 | 47 (0.580) | intergenic (‑177/+90) | ygfF/gcvP | putative NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 3 (0.040) | 3/222 | 7.0 | 3.1% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 94 (1.340) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 1990829 | 98 (1.130) | 4 (0.050) | 4/270 | 7.3 | 4.0% | coding (1149/1212 nt) | tyrP | tyrosine:H(+) symporter |
| ? | NC_000913 | 1990833 = | 95 (1.110) | coding (1153/1212 nt) | tyrP | tyrosine:H(+) symporter | |||||
| * | ? | NC_000913 | 4542682 = | 70 (0.810) | 3 (0.040) | 3/256 | 7.6 | 3.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 87 (1.070) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||