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 21 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 730,537 | 0 | C | T | 68.2% | 4.7 / 14.9 | 22 | R319C (CGC→TGC) | rhsC | rhs element protein RhsC |
| * | NC_000913 | 29,496 | 0 | T | A | 47.5% | 32.9 / 34.6 | 40 | intergenic (+301/‑155) | dapB/carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| * | NC_000913 | 4,604,344 | 0 | C | T | 40.6% | 62.5 / 37.8 | 64 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 1,825,061 | 0 | G | A | 37.5% | 37.6 / 14.7 | 32 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 2,001,918 | 0 | A | C | 34.0% | 76.7 / 22.3 | 50 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| * | NC_000913 | 1,270,009 | 0 | T | A | 32.2% | 134.5 / 92.0 | 90 | intergenic (+86/+229) | rdlB/ldrC | small regulatory antisense RNA RdlB/small toxic polypeptide LdrC |
| * | NC_000913 | 4,101,514 | 0 | G | T | 31.7% | 91.7 / 20.3 | 41 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 3,982,676 | 1 | . | C | 28.8% | 89.4 / 75.6 | 59 | noncoding (71/87 nt) | leuT | tRNA‑Leu |
| * | NC_000913 | 650,809 | 0 | T | G | 27.1% | 98.2 / 12.4 | 48 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 332,991 | 0 | G | T | 26.7% | 110.1 / 17.2 | 45 | L207F (TTG→TTT) | pdeL | DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 3,084,526 | 0 | C | T | 25.3% | 160.5 / 55.2 | 91 | Q462Q (CAG→CAA) | speA | arginine decarboxylase, biosynthetic |
| * | NC_000913 | 2,326,450 | 0 | T | G | 25.0% | 81.2 / 15.7 | 40 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 372,640 | 0 | T | G | 24.6% | 136.6 / 14.3 | 61 | L176V (TTA→GTA) | mhpD | 2‑hydroxypentadienoate hydratase |
| * | NC_000913 | 1,645,034 | 0 | A | C | 23.5% | 104.9 / 13.6 | 51 | intergenic (‑132/+85) | rem/hokD | Qin prophage; protein Rem/Qin prophage; toxic protein HokD |
| * | NC_000913 | 4,098,155 | 0 | A | C | 23.5% | 150.0 / 12.2 | 69 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator RhaS |
| * | NC_000913 | 1,491,098 | 0 | A | C | 23.2% | 154.9 / 11.8 | 69 | Y66S (TAC→TCC) | cybB | cytochrome b561 |
| * | NC_000913 | 4,287,719 | 0 | T | A | 23.1% | 156.0 / 20.2 | 65 | intergenic (‑348/‑45) | acs/nrfA | acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase |
| * | NC_000913 | 3,740,909 | 0 | T | G | 22.9% | 141.2 / 10.9 | 61 | V402G (GTG→GGG) | avtA | valine‑‑pyruvate aminotransferase |
| * | NC_000913 | 3,926,366 | 0 | A | C | 22.3% | 219.1 / 19.5 | 94 | G30G (GGT→GGG) | mioC | flavoprotein MioC |
| * | NC_000913 | 1,577,123 | 0 | A | C | 21.1% | 224.9 / 15.2 | 90 | V166G (GTA→GGA) | yddB | putative TonB‑dependent receptor |
| Marginal new junction evidence (lowest skew 10 of 27 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 374963 | NA (NA) | 14 (0.270) | 9/188 | 3.6 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 23 (0.410) | 10/200 | 3.6 | 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 | = 375059 | NA (NA) | 27 (0.360) +T |
14/272 | 3.8 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375102 = | NA (NA) | 20 (0.330) | 9/214 | 4.1 | NA | noncoding (17/36 nt) | other | REP31d |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 4542690 | 56 (0.730) | 11 (0.150) | 10/256 | 4.6 | 15.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 69 (0.960) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 375001 = | NA (NA) | 9 (0.150) | 7/214 | 4.8 | NA | noncoding (17/36 nt) | other | REP31b |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | 4542682 = | 65 (0.850) | 8 (0.110) | 8/256 | 5.2 | 11.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 69 (0.960) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 7 (0.100) +GAACGCCTTATCCGGT |
7/242 | 5.3 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 555833 | 70 (0.910) | 6 (0.090) | 6/242 | 5.7 | 6.8% | coding (1223/1386 nt) | cysS | cysteine‑‑tRNA ligase |
| ? | NC_000913 | = 556784 | 102 (1.510) | coding (90/213 nt) | ybcJ | putative RNA‑binding protein YbcJ | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 9 (0.120) +T |
7/272 | 5.8 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||