mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 60 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,268 | 0 | T | C | 51.6% | ‑1.0 / 44.6 | 31 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 354,288 | 0 | T | G | 36.6% | 121.3 / 20.9 | 71 | V528G (GTG→GGG) | prpE | propionyl‑CoA synthetase |
| * | NC_000913 | 4,101,514 | 0 | G | T | 34.4% | 45.4 / 10.5 | 32 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 1,825,056 | 0 | G | A | 32.3% | 49.1 / 11.6 | 31 | intergenic (‑119/+84) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 4,604,344 | 0 | C | T | 32.3% | 49.1 / 12.2 | 31 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 469,571 | 0 | A | . | 31.9% | 172.3 / 83.5 | 69 | coding (701/1773 nt) | mdlA | ABC transporter family protein MdlA |
| * | NC_000913 | 2,326,450 | 0 | T | G | 31.7% | 103.9 / 13.3 | 60 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,825,061 | 0 | G | A | 31.2% | 55.2 / 13.9 | 32 | intergenic (‑124/+79) | ves/spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| * | NC_000913 | 635,092 | 0 | A | T | 31.0% | 49.5 / 13.3 | 29 | D95E (GAT→GAA) | ybdM | ParB‑like nuclease domain‑containing protein YbdM |
| * | NC_000913 | 1,435,727 | 0 | G | A | 30.8% | 41.5 / 11.1 | 27 | intergenic (‑108/+33) | uspF/ompN | universal stress protein F/outer membrane porin N |
| * | NC_000913 | 3,003,921 | 0 | T | G | 30.4% | 96.9 / 11.3 | 47 | Y145D (TAT→GAT) | xdhC | putative xanthine dehydrogenase iron‑sulfur‑binding subunit XdhC |
| * | NC_000913 | 4,056,115 | 0 | A | C | 29.8% | 124.5 / 11.5 | 70 | G75G (GGT→GGG) | glnL | protein histidine kinase NtrB |
| * | NC_000913 | 2,745,089 | 0 | A | C | 29.5% | 203.5 / 21.0 | 106 | V84G (GTG→GGG) | trmD | tRNA m(1)G37 methyltransferase |
| * | NC_000913 | 288,382 | 0 | A | C | 29.1% | 166.3 / 12.4 | 103 | T532P (ACC→CCC) | yagH | putative xylosidase/arabinosidase |
| * | NC_000913 | 4,429,990 | 0 | A | T | 28.6% | 89.3 / 13.5 | 49 | M43L (ATG→TTG) | cycA | D‑serine/alanine/glycine/:H(+)symporter |
| * | NC_000913 | 2,377,835 | 0 | G | A | 27.0% | 140.4 / 17.7 | 75 | F475F (TTC→TTT) | menD | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase |
| * | NC_000913 | 3,108,896 | 0 | T | C | 27.0% | 120.8 / 10.5 | 63 | E87G (GAG→GGG) | speC | constitutive ornithine decarboxylase |
| * | NC_000913 | 2,851,654 | 0 | T | G | 26.4% | 151.4 / 14.3 | 73 | G218G (GGT→GGG) | hypB | hydrogenase isoenzymes nickel incorporation protein HypB |
| * | NC_000913 | 1,983,649 | 0 | T | C | 26.3% | 216.1 / 10.1 | 95 | E474G (GAA→GGA) | araG | arabinose ABC transporter ATP binding subunit |
| * | NC_000913 | 422,218 | 0 | C | T | 25.9% | 111.1 / 14.4 | 58 | F411F (TTC→TTT) | proY | putative transporter ProY |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3560353 | 86 (1.160) | 16 (0.230) | 16/452 | 2.0 | 19.6% | intergenic (+487/+269) | rtcR/glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| ? | NC_000913 | 3560479 = | 50 (0.710) | intergenic (+613/+143) | rtcR/glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG | |||||
| * | ? | NC_000913 | = 1861307 | 44 (0.600) | 7 (0.100) | 7/472 | 3.4 | 13.7% | coding (26/1077 nt) | ydjL | putative zinc‑binding dehydrogenase YdjL |
| ? | NC_000913 | 2068941 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 4175240 | 46 (0.620) | 7 (0.090) | 7/476 | 3.5 | 13.2% | intergenic (‑214/‑148) | coaA/thrU | pantothenate kinase/tRNA‑Thr |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 4175236 = | 44 (0.590) | 8 (0.110) | 7/476 | 3.5 | 15.4% | intergenic (‑210/‑152) | coaA/thrU | pantothenate kinase/tRNA‑Thr |
| ? | NC_000913 | = 4499511 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1858980 | 28 (0.380) | 6 (0.080) | 6/476 | 3.7 | 17.6% | coding (1250/1380 nt) | ydjK | putative transporter YdjK |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 2540083 | 83 (1.120) | 3 (0.040) | 3/474 | 4.5 | 3.8% | coding (732/1098 nt) | cysA | sulfate/thiosulfate ABC transporter ATP binding subunit |
| ? | NC_000913 | 4067196 = | 70 (0.950) | intergenic (‑2/+44) | yihP/yihQ | putative 2,3‑dihydroxypropane‑1‑sulfonate export protein/sulfoquinovosidase | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 3 (0.040) | 3/476 | 4.5 | 3.5% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 336909 = | 83 (1.120) | coding (132/1548 nt) | yahF | putative acyl‑CoA synthetase YahF | |||||