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 23 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 42.9% | 61.7 / 52.3 | 70 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,111,747 | 0 | G | T | 34.3% | 75.4 / 23.4 | 35 | N156K (AAC→AAA) | yiiQ | DUF1454 domain‑containing protein YiiQ |
| * | NC_000913 | 1,491,103 | 0 | A | C | 34.2% | 110.7 / 30.3 | 76 | T68P (ACC→CCC) | cybB | cytochrome b561 |
| * | NC_000913 | 3,556,207 | 0 | T | C | 32.3% | 43.9 / 12.1 | 31 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,628,625 | 0 | A | C | 28.8% | 97.1 / 17.9 | 52 | V105G (GTC→GGC) | pdeF | cyclic di‑GMP phosphodiesterase PdeF |
| * | NC_000913 | 4,296,060 | 0 | C | T | 28.1% | 149.6 / 56.1 | 82 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 29,496 | 0 | T | A | 27.6% | 123.6 / 28.7 | 58 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,568,504 | 0 | T | G | 27.4% | 210.1 / 11.2 | 106 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 2,326,450 | 0 | T | G | 27.3% | 113.6 / 39.5 | 66 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,628,649 | 0 | A | C | 26.2% | 134.3 / 12.5 | 65 | intergenic (+102/+206) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| * | NC_000913 | 646,747 | 0 | T | G | 26.1% | 133.1 / 31.0 | 69 | T255P (ACC→CCC) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 4,429,984 | 0 | T | G | 25.0% | 133.0 / 19.5 | 64 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 650,809 | 0 | T | G | 24.7% | 185.0 / 22.2 | 89 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 3,781,120 | 0 | T | C | 24.4% | 80.4 / 10.2 | 41 | intergenic (+103/‑95) | lldD/trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| * | NC_000913 | 786,855 | 0 | A | C | 24.1% | 117.9 / 12.5 | 54 | G247G (GGT→GGG) | gpmA | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| * | NC_000913 | 646,760 | 0 | T | C | 23.9% | 137.6 / 22.6 | 67 | K250K (AAA→AAG) | citG | triphosphoribosyl‑dephospho‑CoA synthase |
| * | NC_000913 | 372,640 | 0 | T | G | 23.5% | 136.9 / 20.5 | 68 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 501,572 | 0 | A | C | 22.6% | 121.4 / 10.5 | 53 | V556G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 501,575 | 0 | A | C | 22.6% | 120.6 / 10.4 | 53 | V555G (GTG→GGG) | ybaL | putative transporter YbaL |
| * | NC_000913 | 3,240,985 | 0 | T | G | 22.4% | 130.8 / 10.9 | 58 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 83 (0.940) | 14 (0.170) | 13/258 | 4.1 | 15.5% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 75 (0.900) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 75 (0.850) | 8 (0.100) | 7/258 | 5.9 | 9.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 75 (0.900) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 4 (0.060) +32 bp |
4/212 | 6.4 | 100% | intergenic (‑305/+16) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 291404 | NA (NA) | 4 (0.060) +29 bp |
4/218 | 6.5 | 100% | intergenic (‑58/‑96) | insA‑3/yagJ | IS1 protein InsA/CP4‑6 prophage; protein YagJ |
| ? | NC_000913 | = 1978502 | 0 (0.000) | intergenic (‑305/+16) | flhD/insB‑5 | DNA‑binding transcriptional dual regulator FlhD/IS1 protein InsB | |||||
| * | ? | NC_000913 | = 1050545 | NA (NA) | 4 (0.050) | 4/274 | 7.5 | 18.3% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1979302 = | 18 (0.200) | intergenic (‑87/‑451) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | = 382354 | NA (NA) | 4 (0.050) | 4/274 | 7.5 | NA | noncoding (1095/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 382358 = | NA (NA) | noncoding (1099/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 4 (0.050) | 4/276 | 7.6 | 18.2% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1979302 = | 18 (0.200) | intergenic (‑87/‑451) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 290634 = | NA (NA) | 4 (0.050) | 4/276 | 7.6 | 18.2% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1979302 = | 18 (0.200) | intergenic (‑87/‑451) | insA‑5/uspC | IS1 protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | = 1354143 | 59 (0.660) | 3 (0.040) | 3/256 | 7.8 | 4.4% | coding (376/891 nt) | sapC | putrescine ABC exporter membrane protein SapC |
| ? | NC_000913 | = 1354235 | 75 (0.910) | coding (284/891 nt) | sapC | putrescine ABC exporter membrane protein SapC | |||||
| * | ? | NC_000913 | 381681 = | NA (NA) | 3 (0.040) | 3/258 | 7.8 | NA | noncoding (422/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381753 = | NA (NA) | noncoding (494/1331 nt) | IS2 | repeat region | |||||