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 66 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,813,174 | 0 | A | C | 58.0% | 12.1 / 67.3 | 51 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,813,175 | 0 | A | G | 56.9% | 17.1 / 63.4 | 51 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 5,227,990 | 0 | A | T | 56.5% | ‑5.7 / 12.9 | 29 | L435Q (CTG→CAG) | PP_4603 | transposase |
| * | NC_002947 | 699,725 | 0 | A | G | 54.3% | 35.6 / inf | 432 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,332,076 | 0 | C | T | 50.2% | 254.1 / inf | 547 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,353,698 | 0 | A | G | 48.6% | 307.8 / inf | 633 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 40.4% | 431.8 / inf | 559 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,813,180 | 0 | C | T | 30.8% | 63.9 / 43.2 | 52 | intergenic (‑295/‑260) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,813,181 | 0 | G | T | 30.8% | 69.3 / 47.1 | 52 | intergenic (‑296/‑259) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 195,559 | 0 | C | A | 29.5% | 691.1 / 279.4 | 385 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 3,471,833 | 0 | T | G | 29.4% | 545.3 / 80.9 | 349 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947 | 4,882,318 | 0 | G | C | 29.1% | 538.6 / 97.5 | 262 | intergenic (‑372/‑28) | pucM/puuE | 5‑hydroxyisourate hydrolase/allantoinase |
| * | NC_002947 | 196,879 | 0 | G | A | 28.9% | 195.4 / 94.9 | 124 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,358,202 | 0 | T | G | 27.7% | 228.8 / 32.5 | 141 | V112G (GTG→GGG) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947 | 4,813,183 | 0 | G | C | 26.2% | 73.4 / 29.3 | 42 | intergenic (‑298/‑257) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,163,459 | 0 | T | G | 26.1% | 496.0 / 41.2 | 304 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947 | 4,345,068 | 0 | A | T | 25.7% | 272.4 / 58.3 | 177 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 3,877,805 | 0 | T | G | 25.1% | 492.2 / 28.2 | 237 | Q443P (CAG→CCG) | PP_3421 | sensor histidine kinase |
| * | NC_002947 | 220,563 | 0 | A | C | 24.9% | 675.3 / 26.1 | 315 | intergenic (+20/‑108) | PP_0168/PP_5431 | putative surface adhesion protein/hypothetical protein |
| * | NC_002947 | 5,729,306 | 0 | T | G | 24.9% | 529.7 / 31.0 | 286 | intergenic (‑203/+91) | PP_5024/opgH | amino acid ABC transporter substrate‑binding protein/glucans biosynthesis glucosyltransferase H |
| Marginal new junction evidence (lowest skew 10 of 460 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4813168 = | 49 (0.120) | 174 (0.560) | 62/226 | 7.8 | 65.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993940 | 150 (0.480) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5206564 | 232 (0.570) | 86 (0.220) | 57/290 | 12.5 | 33.1% | intergenic (‑53/‑127) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | 5206663 = | 120 (0.300) | intergenic (‑152/‑28) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | = 4813173 | 23 (0.060) | 155 (0.410) | 50/272 | 13.1 | 52.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 256 (0.680) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 392 (0.960) | 97 (0.280) | 42/256 | 14.3 | 36.4% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4813153 | 1 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 1785057 | 193 (0.470) | 56 (0.140) | 46/282 | 14.7 | 25.8% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | 1785120 = | 139 (0.360) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | = 5993776 | 279 (0.680) | 44 (0.110) | 33/280 | 18.5 | 15.2% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5993968 = | 229 (0.590) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4591012 = | 216 (0.530) | 16 (0.050) | 8/220 | 26.8 | 10.8% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4591116 = | 105 (0.350) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 2055551 = | 291 (0.710) | 15 (0.050) | 8/222 | 26.9 | 7.3% | intergenic (‑52/+123) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947 | 2055661 = | 164 (0.540) | intergenic (‑162/+13) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947 | 1431756 = | NA (NA) | 40 (0.100) | 13/290 | 27.8 | NA | coding (698/1422 nt) | PP_1250 | group II intron‑encoding maturase |
| ? | NC_002947 | 1431816 = | NA (NA) | coding (758/1422 nt) | PP_1250 | group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | = 2263051 | NA (NA) | 43 (0.110) | 12/280 | 27.9 | 23.0% | intergenic (+114/‑278) | PP_1990/asd | transposase/aspartate‑semialdehyde dehydrogenase |
| ? | NC_002947 | = 2263144 | 152 (0.370) | intergenic (+207/‑185) | PP_1990/asd | transposase/aspartate‑semialdehyde dehydrogenase | |||||