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 | 42.2% | 75.0 / 50.3 | 71 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 237,040 | 0 | G | T | 42.2% | 148.1 / 188.0 | 135 | intergenic (+33/‑295) | aspV/yafT | tRNA‑Asp/lipoprotein YafT |
| * | NC_000913 | 4,111,747 | 0 | G | T | 36.1% | 134.2 / 57.7 | 72 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 33.3% | 65.9 / 28.6 | 48 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 29.1% | 155.1 / 32.6 | 79 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,550,663 | 0 | A | C | 27.9% | 86.9 / 13.8 | 43 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 4,111,752 | 0 | T | C | 25.6% | 157.6 / 14.2 | 82 | K155E (AAA→GAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 2,204,240 | 0 | C | A | 25.6% | 326.1 / 96.9 | 125 | A90E (GCA→GAA) | yehK | uncharacterized protein YehK |
| * | NC_000913 | 3,556,207 | 0 | T | C | 25.0% | 100.4 / 14.8 | 52 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 888,014 | 0 | T | G | 24.6% | 133.7 / 14.2 | 61 | noncoding (44/81 nt) | rybB | small regulatory RNA RybB |
| * | NC_000913 | 4,568,504 | 0 | T | G | 23.4% | 327.7 / 21.5 | 145 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 23.4% | 194.7 / 52.2 | 94 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,628,625 | 0 | A | C | 22.4% | 120.8 / 11.1 | 49 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 445,558 | 0 | A | C | 22.2% | 118.9 / 27.7 | 54 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 650,809 | 0 | T | G | 21.8% | 195.7 / 12.8 | 78 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,001,918 | 0 | A | C | 21.3% | 183.4 / 22.5 | 75 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 3,206,444 | 0 | T | A | 20.8% | 112.5 / 13.1 | 53 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 2,326,450 | 0 | T | G | 20.5% | 198.8 / 26.9 | 78 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 3,401,459 | 0 | T | C | 20.0% | 166.2 / 11.9 | 75 | D625G (GAT→GGT) | csrD | regulator of CsrB and CsrC decay |
| Marginal new junction evidence (lowest skew 10 of 14 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 78 (0.650) | 24 (0.210) | 19/258 | 3.9 | 22.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 96 (0.850) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 81 (0.670) | 13 (0.120) | 11/258 | 5.8 | 13.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 96 (0.850) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 11 (0.120) | 7/202 | 6.0 | 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 | 1207790 = | 160 (1.330) | 10 (0.090) | 9/244 | 6.2 | 7.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 99 (0.930) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 6 (0.060) | 6/224 | 7.0 | 4.2% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 136 (1.390) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 16 (0.140) | 7/260 | 7.3 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 1622821 | 43 (0.410) | 7 (0.060) +AAACCGCCAGT |
4/220 | 7.9 | 13.2% | noncoding (94/98 nt) | mgrR | small regulatory RNA MgrR |
| ? | NC_000913 | 1622822 = | 51 (0.420) | noncoding (93/98 nt) | mgrR | small regulatory RNA MgrR | |||||
| * | ? | NC_000913 | = 25796 | NA (NA) | 7 (0.060) | 5/274 | 8.5 | NA | noncoding (1/34 nt) | other | REP2b |
| ? | NC_000913 | 377322 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 3067468 = | 108 (0.890) | 3 (0.030) | 3/254 | 9.2 | 2.7% | coding (613/741 nt) | yggE | uncharacterized protein YggE |
| ? | NC_000913 | 3067560 = | 113 (1.020) | coding (521/741 nt) | yggE | uncharacterized protein YggE | |||||
| * | ? | NC_000913 | = 4473666 | 140 (1.160) | 4 (0.030) | 3/270 | 9.5 | 2.8% | coding (388/714 nt) | bdcA | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| ? | NC_000913 | 4473670 = | 137 (1.160) | coding (384/714 nt) | bdcA | c‑di‑GMP‑binding biofilm dispersal mediator protein | |||||