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 (highest frequency 20 of 234 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,394,808 | 0 | C | G | 65.2% | ‑6.8 / 16.7 | 23 | R58P (CGG→CCG) | PP_3868 | group II intron‑encoding maturase |
| * | NC_002947 | 4,350,671 | 0 | A | G | 52.4% | 270.2 / inf | 1357 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 50.4% | 481.8 / inf | 1172 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,725 | 0 | A | G | 50.2% | 142.6 / inf | 941 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,810,147 | 0 | A | C | 46.8% | 38.0 / 255.3 | 173 | 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 | 46.8% | 34.8 / 230.3 | 173 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 2,284,735 | 0 | T | G | 44.8% | 272.0 / inf | 654 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,284,744 | 0 | C | A | 42.4% | 412.0 / inf | 617 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,342,049 | 0 | A | G | 41.4% | 304.8 / inf | 361 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,050 | 0 | C | T | 41.3% | 303.0 / inf | 361 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 2,284,740 | 0 | G | C | 41.2% | 437.1 / inf | 591 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 2,284,739 | 0 | G | C | 41.1% | 468.9 / inf | 591 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,342,048 | 0 | C | T | 41.0% | 306.2 / inf | 362 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,047 | 0 | A | G | 40.9% | 324.4 / inf | 369 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,042 | 0 | G | C | 39.6% | 451.7 / inf | 401 | intergenic (+61/‑270) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 195,634 | 0 | C | T | 39.6% | 1087.8 / inf | 1357 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,013,252 | 0 | T | G | 39.4% | 511.9 / inf | 552 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 4,342,056 | 0 | A | T | 39.1% | 432.7 / inf | 389 | intergenic (+75/‑256) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,055 | 0 | G | C | 38.6% | 469.6 / inf | 394 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 4,342,041 | 0 | A | T | 38.0% | 471.1 / inf | 433 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 1230 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 652785 | 739 (0.940) | 342 (0.510) | 107/244 | 7.2 | 51.8% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4810126 | 1 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4810146 | 93 (0.120) | 341 (0.470) | 108/260 | 8.2 | 45.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5990743 = | 740 (1.030) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4810146 | 93 (0.120) | 294 (0.440) | 91/244 | 9.8 | 43.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990927 | 692 (1.020) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 5479060 = | 489 (0.620) | 122 (0.220) | 54/202 | 14.4 | 30.2% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5479159 = | 217 (0.390) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | 4810141 = | 139 (0.180) | 213 (0.330) | 64/232 | 14.5 | 36.4% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5990757 = | 631 (0.980) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 4587985 = | 497 (0.630) | 140 (0.240) | 54/208 | 15.0 | 32.8% | intergenic (+102/+115) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4588089 = | 211 (0.370) | intergenic (+206/+11) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 5916135 = | 441 (0.560) | 176 (0.280) | 60/228 | 15.1 | 32.0% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | 5916231 = | 395 (0.630) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | = 1970782 | 682 (0.870) | 159 (0.240) | 65/244 | 15.2 | 21.2% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947 | = 1970844 | 596 (0.880) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947 | 4161049 = | 535 (0.680) | 141 (0.200) | 65/252 | 15.8 | 23.2% | intergenic (+31/‑178) | PP_3661/PP_3662 | membrane protein/hypothetical protein |
| ? | NC_002947 | 4161109 = | 457 (0.650) | intergenic (+91/‑118) | PP_3661/PP_3662 | membrane protein/hypothetical protein | |||||
| * | ? | NC_002947 | 6008517 = | 391 (0.500) | 201 (0.340) | 52/212 | 15.9 | 44.2% | intergenic (+7/+92) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947 | 6008601 = | 216 (0.370) | intergenic (+91/+8) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||