mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
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_002947 | 1,499,497 | 1 | . | C | 71.5% | 141.0 / 176.8 | 159 | intergenic (+74/‑90) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| * | NC_002947 | 1,499,498 | 0 | T | G | 71.5% | 74.6 / 145.2 | 159 | intergenic (+75/‑89) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| * | NC_002947 | 4,741,229 | 0 | A | C | 57.9% | 12.5 / 33.6 | 38 | intergenic (+466/+287) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,231 | 0 | C | G | 52.6% | ‑0.8 / 64.8 | 38 | intergenic (+468/+285) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,237 | 0 | C | G | 52.6% | ‑0.3 / 63.2 | 38 | intergenic (+474/+279) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,239 | 0 | A | G | 52.6% | 37.6 / 43.5 | 38 | intergenic (+476/+277) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,244 | 0 | C | G | 52.6% | ‑2.1 / 70.0 | 38 | intergenic (+481/+272) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,245 | 0 | A | C | 52.6% | 21.5 / 71.0 | 38 | intergenic (+482/+271) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 699,722 | 0 | A | G | 50.0% | 318.4 / 71.9 | 280 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,741,232 | 0 | C | T | 47.4% | 53.0 / 57.4 | 38 | intergenic (+469/+284) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,235 | 0 | C | T | 47.4% | 17.1 / 46.6 | 38 | intergenic (+472/+281) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,238 | 0 | C | G | 47.4% | ‑5.6 / 63.9 | 38 | intergenic (+475/+278) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,240 | 0 | A | C | 47.4% | 26.9 / 10.4 | 38 | intergenic (+477/+276) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,241 | 0 | C | T | 47.4% | 46.9 / 55.4 | 38 | intergenic (+478/+275) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,348,705 | 0 | A | G | 45.9% | 255.6 / 136.0 | 270 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,121 | 0 | C | T | 42.9% | 200.7 / inf | 345 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,741,228 | 1 | . | C | 42.1% | 5.9 / 86.4 | 38 | intergenic (+465/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 195,634 | 0 | C | T | 36.1% | 19.0 / 183.5 | 241 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,499,498 | 1 | . | G | 28.3% | 121.2 / 224.4 | 159 | intergenic (+75/‑89) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| * | NC_002947 | 2,087,210 | 0 | T | G | 25.2% | 284.8 / 59.7 | 211 | intergenic (+23/+895) | PP_1865/aroH | transposase/3‑deoxy‑7‑phosphoheptulonate synthase |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808174 = | 7 (0.040) | 28 (0.220) | 16/166 | 9.7 | 36.4% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988935 | 93 (0.720) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5988771 | 117 (0.630) | 16 (0.090) | 16/220 | 12.2 | 12.3% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5988963 = | 120 (0.700) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808174 | 4 (0.020) | 28 (0.160) | 15/220 | 12.6 | 85.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 4808189 = | 6 (0.030) | intergenic (‑298/‑257) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 652783 | 202 (1.090) | 17 (0.130) | 9/166 | 12.7 | 19.0% | coding (1960/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | 4808209 = | 3 (0.020) | intergenic (‑318/‑237) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 4808174 = | 7 (0.040) | 20 (0.140) | 10/184 | 13.1 | 32.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988779 = | 79 (0.550) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4808179 | 3 (0.020) | 28 (0.150) | 10/234 | 15.3 | 80.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 4808194 = | 11 (0.060) | intergenic (‑303/‑252) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808166 | 4 (0.020) | 15 (0.090) +AGCGCCG |
7/206 | 15.7 | 75.6% | intergenic (‑275/‑280) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 4808179 | 6 (0.030) | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 2478415 = | 36 (0.190) | 6 (0.040) | 5/196 | 16.6 | 17.9% | coding (112/444 nt) | PP_2172 | hypothetical protein |
| ? | NC_002947 | = 2478405 | 25 (0.160) | coding (102/444 nt) | PP_2172 | hypothetical protein | |||||
| * | ? | NC_002947 | = 3534746 | 206 (1.120) | 7 (0.040) | 6/222 | 17.0 | 3.6% | intergenic (+33/‑122) | atoB/PP_3124 | 3‑oxoacid CoA‑transferase subunit B/short chain fatty acid transporter |
| ? | NC_002947 | 3534791 = | 184 (1.060) | intergenic (+78/‑77) | atoB/PP_3124 | 3‑oxoacid CoA‑transferase subunit B/short chain fatty acid transporter | |||||
| * | ? | NC_002947 | 2478409 = | 35 (0.190) | 8 (0.060) | 3/184 | 17.5 | 25.3% | coding (106/444 nt) | PP_2172 | hypothetical protein |
| ? | NC_002947 | = 2478405 | 20 (0.140) | coding (102/444 nt) | PP_2172 | hypothetical protein | |||||