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 148 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,127 | 0 | C | T | 52.5% | 87.2 / inf | 357 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,350,671 | 0 | A | G | 48.5% | 188.4 / inf | 434 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,810,147 | 0 | A | C | 46.3% | 3.3 / 60.6 | 42 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,810,148 | 0 | A | G | 45.2% | 10.8 / 51.8 | 42 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 699,725 | 0 | A | G | 43.7% | 152.9 / inf | 311 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 358,093 | 0 | T | C | 42.9% | 48.2 / 91.0 | 79 | intergenic (+58/‑72) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 1,013,252 | 0 | T | G | 42.1% | 111.0 / 204.8 | 152 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,544,543 | 0 | G | C | 41.9% | 128.4 / 221.0 | 162 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,546 | 0 | T | G | 41.8% | 124.5 / 219.2 | 165 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 2,284,735 | 0 | T | G | 41.3% | 105.2 / 205.6 | 155 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 358,097 | 0 | A | G | 41.2% | 58.3 / 88.5 | 80 | intergenic (+62/‑68) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 358,094 | 0 | G | A | 41.0% | 54.1 / 88.7 | 79 | intergenic (+59/‑71) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 1,544,536 | 0 | C | G | 40.7% | 153.5 / 219.6 | 162 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,541 | 0 | C | G | 40.7% | 154.9 / 218.0 | 162 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,531 | 0 | C | A | 40.6% | 152.7 / 209.5 | 170 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,534 | 0 | G | C | 40.5% | 168.2 / 224.8 | 168 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 195,634 | 0 | C | T | 40.4% | 307.6 / inf | 394 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 358,099 | 0 | C | T | 40.2% | 61.9 / 93.1 | 82 | intergenic (+64/‑66) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 4,844,863 | 0 | C | . | 40.1% | 306.5 / 247.2 | 147 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 1,013,245 | 0 | G | C | 39.6% | 182.7 / 214.6 | 165 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 432 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4810141 = | 33 (0.130) | 84 (0.450) | 42/222 | 6.6 | 51.2% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990913 | 135 (0.720) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4810146 | 23 (0.090) | 130 (0.580) | 39/268 | 9.8 | 55.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5990743 = | 189 (0.840) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 227 (0.920) | 69 (0.330) | 35/252 | 10.1 | 41.4% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4810126 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4898365 | 122 (0.500) | 49 (0.230) | 24/250 | 13.6 | 29.1% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4898412 | 134 (0.640) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 4587985 = | 108 (0.440) | 36 (0.200) | 19/216 | 13.6 | 35.5% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4588089 = | 51 (0.280) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 4810141 = | 33 (0.130) | 60 (0.300) | 21/240 | 14.3 | 39.6% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5990757 = | 156 (0.770) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4810146 | 23 (0.090) | 99 (0.470) | 22/252 | 14.5 | 50.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990927 | 176 (0.830) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 5479060 = | 101 (0.410) | 41 (0.230) | 16/210 | 14.6 | 39.1% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5479159 = | 55 (0.310) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | = 5203585 | 66 (0.270) | 33 (0.180) | 17/218 | 14.7 | 39.7% | intergenic (‑101/‑79) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | = 5203606 | 51 (0.280) | intergenic (‑122/‑58) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | 1967188 = | 112 (0.460) | 39 (0.210) | 17/226 | 15.2 | 33.8% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967284 = | 66 (0.350) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||