mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 4,604,344 | 0 | C | T | 42.6% | 54.2 / 38.6 | 54 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 646,747 | 0 | T | G | 34.2% | 52.0 / 27.2 | 41 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 34.0% | 63.8 / 35.8 | 50 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,111,747 | 0 | G | T | 32.1% | 62.0 / 16.9 | 28 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,001,918 | 0 | A | C | 31.7% | 65.3 / 16.2 | 41 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,296,060 | 0 | C | T | 29.6% | 119.6 / 53.0 | 71 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 4,101,507 | 0 | T | G | 29.2% | 85.3 / 11.0 | 48 | intergenic (+77/‑183) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 753,125 | 0 | T | A | 28.9% | 93.2 / 16.2 | 45 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,550,663 | 0 | A | C | 26.5% | 93.0 / 15.6 | 49 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 3,206,435 | 0 | C | T | 24.3% | 73.4 / 13.6 | 37 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 646,760 | 0 | T | C | 23.5% | 103.8 / 15.5 | 51 | K250K (AAA→AAG) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 22.9% | 136.2 / 13.0 | 48 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,926,366 | 0 | A | C | 22.2% | 143.4 / 10.2 | 63 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 4,429,984 | 0 | T | G | 21.8% | 124.2 / 12.9 | 55 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 3,844,219 | 0 | T | G | 21.2% | 147.6 / 13.4 | 66 | F86V (TTT→GTT) | adeD | adenine deaminase |
| * | NC_000913 | 3,404,215 | 0 | T | G | 20.9% | 86.5 / 10.7 | 43 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 3,240,985 | 0 | T | G | 20.6% | 144.3 / 12.4 | 64 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 372,640 | 0 | T | G | 20.4% | 100.4 / 12.3 | 49 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 1,068,173 | 0 | T | G | 20.0% | 152.6 / 11.2 | 66 | G31G (GGT→GGG) | ymdF | conserved protein YmdF |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 52 (0.750) | 14 (0.220) | 12/258 | 3.6 | 18.7% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 73 (1.120) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 53 (0.760) | 7 (0.110) | 6/258 | 5.5 | 10.3% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 73 (1.120) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3620868 | NA (NA) | 4 (0.060) | 4/254 | 6.4 | 9.8% | coding (1677/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3621008 | 40 (0.570) | coding (1817/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 1181324 = | 40 (0.570) | 4 (0.060) | 4/276 | 6.7 | 9.1% | coding (402/462 nt) | ymfA | putative inner membrane protein |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 665443 | 67 (0.960) | 4 (0.060) | 4/276 | 6.7 | 5.5% | coding (871/1113 nt) | mrdB | SEDS family protein MrdB |
| ? | NC_000913 | 665447 = | 70 (1.010) | coding (867/1113 nt) | mrdB | SEDS family protein MrdB | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 4 (0.060) | 4/276 | 6.7 | 9.1% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1181324 = | 40 (0.570) | coding (402/462 nt) | ymfA | putative inner membrane protein | |||||
| * | ? | NC_000913 | 2728258 = | NA (NA) | 3 (0.050) | 3/262 | 7.0 | NA | noncoding (927/2904 nt) | rrlG | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 226685 | 38 (0.550) | 3 (0.050) | 3/262 | 7.0 | 7.7% | noncoding (927/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | NC_000913 | 2728336 = | NA (NA) | noncoding (849/2904 nt) | rrlG | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 2465466 = | 61 (0.880) | 3 (0.040) | 3/266 | 7.1 | 4.6% | coding (166/933 nt) | yfdC | inner membrane protein YfdC |
| ? | NC_000913 | = 2465629 | 67 (1.000) | coding (329/933 nt) | yfdC | inner membrane protein YfdC | |||||
| * | ? | NC_000913 | 4022196 = | 59 (0.850) | 3 (0.040) | 3/274 | 7.2 | 4.9% | coding (252/270 nt) | tatA | twin arginine protein translocation system ‑ TatA protein |
| ? | NC_000913 | 4022209 = | 57 (0.820) | coding (265/270 nt) | tatA | twin arginine protein translocation system ‑ TatA protein | |||||