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 | 4,568,504 | 0 | T | G | 42.9% | 94.0 / 11.5 | 63 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 1,825,061 | 0 | G | A | 37.9% | 35.8 / 16.2 | 29 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 3,206,435 | 0 | C | T | 30.8% | 37.0 / 10.4 | 26 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 28.3% | 97.7 / 13.7 | 46 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.7% | 89.1 / 11.5 | 38 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 374,986 | 0 | T | C | 21.4% | 131.2 / 34.6 | 70 | intergenic (+105/‑473) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| 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 | 374922 = | NA (NA) | 9 (0.230) | 5/202 | 3.4 | 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 | 375124 = | NA (NA) | 4 (0.110) | 4/192 | 3.6 | NA | intergenic (+243/‑335) | 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 | 608007 = | NA (NA) | 4 (0.090) | 4/224 | 4.1 | 7.4% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 50 (1.140) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 375059 | NA (NA) | 5 (0.090) +T |
5/274 | 4.3 | NA | noncoding (28/34 nt) | other | REP31c |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 4542690 | 58 (1.070) | 4 (0.080) | 4/258 | 4.5 | 7.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 50 (0.990) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3848434 | 54 (1.000) | 4 (0.080) | 4/258 | 4.5 | 7.2% | coding (191/1320 nt) | uhpC | inner membrane protein sensing glucose‑6‑phosphate |
| ? | NC_000913 | = 3848546 | 53 (1.050) | coding (79/1320 nt) | uhpC | inner membrane protein sensing glucose‑6‑phosphate | |||||
| * | ? | NC_000913 | = 375246 | NA (NA) | 3 (0.060) +GAACGCCTTATCCGGT |
3/244 | 4.8 | NA | noncoding (13/34 nt) | other | REP31g |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 3888183 | 45 (0.870) | 3 (0.060) +GGTAA |
3/254 | 5.0 | 6.1% | coding (1356/1365 nt) | mnmE | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit |
| ? | NC_000913 | 3888184 = | 49 (0.910) | coding (1357/1365 nt) | mnmE | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit | |||||
| * | ? | NC_000913 | 1643615 = | 59 (1.090) | 3 (0.060) | 3/256 | 5.0 | 5.7% | coding (690/1050 nt) | ydfU | Qin prophage; protein YdfU |
| ? | NC_000913 | 1643805 = | 45 (0.900) | coding (500/1050 nt) | ydfU | Qin prophage; protein YdfU | |||||
| * | ? | NC_000913 | 1014929 = | 56 (1.040) | 3 (0.060) | 3/260 | 5.0 | 5.3% | coding (34/564 nt) | pqiC | intermembrane transport lipoprotein PqiC |
| ? | NC_000913 | 1015018 = | 54 (1.060) | coding (123/564 nt) | pqiC | intermembrane transport lipoprotein PqiC | |||||