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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,309,454 | 0 | G | T | 71.4% | 110.5 / 84.6 | 77 | I272I (ATC→ATA) | kch | K(+) channel Kch |
| * | NC_000913 | 2,001,918 | 0 | A | C | 40.0% | 49.2 / 15.3 | 35 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 4,604,344 | 0 | C | T | 38.5% | 53.9 / 29.0 | 52 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 4,568,504 | 0 | T | G | 29.7% | 189.8 / 10.6 | 92 | 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% | 64.7 / 13.0 | 33 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 29,496 | 0 | T | A | 25.0% | 98.1 / 15.3 | 44 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 3,404,215 | 0 | T | G | 25.0% | 144.7 / 19.0 | 64 | G244G (GGT→GGG) | yhdH | acrylyl‑CoA reductase |
| * | NC_000913 | 1,435,727 | 0 | G | A | 22.9% | 72.8 / 10.6 | 35 | intergenic (‑108/+33) | uspF/ompN | nucleotide binding filament protein/outer membrane porin N |
| * | NC_000913 | 753,125 | 0 | T | A | 22.7% | 149.8 / 20.2 | 67 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 2,667,126 | 0 | A | C | 22.4% | 108.7 / 11.9 | 50 | Y241D (TAT→GAT) | hcaT | putative 3‑phenylpropionate transporter |
| * | NC_000913 | 1,645,034 | 0 | A | C | 22.2% | 128.2 / 12.5 | 54 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 4,429,984 | 0 | T | G | 22.0% | 151.4 / 13.5 | 59 | L41V (TTG→GTG) | cycA | serine/alanine/glycine/cycloserine:H(+)symporter |
| * | NC_000913 | 377,374 | 0 | T | C | 21.1% | 556.7 / 161.9 | 284 | intergenic (+63/+161) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 753,114 | 0 | G | T | 21.1% | 191.4 / 11.2 | 71 | intergenic (‑319/+71) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 4,098,155 | 0 | A | C | 21.1% | 224.3 / 10.1 | 90 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 1,428,700 | 0 | A | G | 20.4% | 205.4 / 49.2 | 98 | D9D (GAT→GAC) | insH‑5 | Rac prophage; IS5 transposase and trans‑activator |
| * | NC_000913 | 3,926,366 | 0 | A | C | 20.0% | 179.3 / 12.4 | 70 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| Marginal new junction evidence (lowest skew 10 of 36 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 375246 | NA (NA) | 21 (0.310) +GAACGCCTTATCCGGT |
11/244 | 3.6 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375183 = | NA (NA) | 15 (0.230) | 10/238 | 3.7 | NA | intergenic (+302/‑276) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 15 (0.250) | 8/224 | 4.1 | 19.7% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 61 (1.000) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | 375023 = | NA (NA) | 5 (0.100) | 5/192 | 4.6 | NA | intergenic (+142/‑436) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377530 = | NA (NA) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 377321 = | NA (NA) | 20 (0.270) | 8/268 | 4.8 | NA | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | = 508817 | NA (NA) | noncoding (2/34 nt) | other | REP48e | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 11 (0.150) +T |
8/274 | 4.8 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 4542690 | 57 (0.760) | 11 (0.160) | 7/258 | 4.9 | 14.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 79 (1.120) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 59 (0.780) | 6 (0.090) | 6/258 | 5.3 | 8.2% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 79 (1.120) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 25796 | NA (NA) | 18 (0.240) | 6/274 | 5.5 | 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 | 15387 = | NA (NA) | 4 (0.070) | 4/224 | 5.6 | 10.3% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 16732 = | 35 (0.570) | intergenic (+175/+19) | insL‑1/hokC | IS186/IS421 transposase/protein HokC | |||||