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 63 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,332,076 | 0 | C | T | 55.8% | 66.6 / inf | 514 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,813,174 | 0 | A | C | 53.4% | 3.0 / 88.6 | 58 | 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 | 53.4% | 5.1 / 80.9 | 58 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 5,227,990 | 0 | A | C | 52.9% | ‑6.4 / 18.4 | 23 | L435R (CTG→CGG) | PP_4603 | transposase |
| * | NC_002947 | 4,353,698 | 0 | A | G | 46.0% | 447.4 / inf | 691 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,725 | 0 | A | G | 42.2% | 283.1 / inf | 419 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 38.1% | 477.6 / inf | 538 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,228,014 | 0 | G | C | 35.5% | ‑5.5 / 12.2 | 31 | A427G (GCT→GGT) | PP_4603 | transposase |
| * | NC_002947 | 4,882,318 | 0 | G | C | 30.7% | 544.4 / 115.5 | 274 | intergenic (‑372/‑28) | pucM/puuE | 5‑hydroxyisourate hydrolase/allantoinase |
| * | NC_002947 | 4,345,068 | 0 | A | T | 29.0% | 228.0 / 97.9 | 163 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,798,394 | 0 | C | G | 28.6% | 70.4 / 34.0 | 42 | F207L (TTC→TTG) | bamA‑I | outer membrane protein assembly factor |
| * | NC_002947 | 4,813,180 | 0 | C | T | 27.8% | 82.6 / 37.6 | 54 | 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 | 27.8% | 94.5 / 35.6 | 54 | intergenic (‑296/‑259) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,163,459 | 0 | T | G | 25.9% | 514.7 / 54.5 | 331 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947 | 3,471,833 | 0 | T | G | 25.8% | 674.0 / 79.0 | 387 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947 | 195,559 | 0 | C | A | 25.6% | 779.4 / 246.7 | 398 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,549,350 | 0 | C | G | 25.6% | 744.8 / 96.1 | 344 | A388G (GCG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947 | 197,590 | 0 | T | C | 25.1% | 896.7 / 301.8 | 468 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,206,967 | 0 | A | C | 24.8% | 831.1 / 36.1 | 356 | Q139P (CAG→CCG) | xcpW | type II secretion pathway protein XcpW |
| * | NC_002947 | 4,358,202 | 0 | T | G | 24.7% | 280.5 / 27.7 | 154 | V112G (GTG→GGG) | yrpB | 2‑nitropropane dioxygenase |
| Marginal new junction evidence (lowest skew 10 of 540 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4813168 = | 52 (0.120) | 166 (0.520) | 58/226 | 8.4 | 60.4% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993940 | 178 (0.560) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5206564 | 240 (0.570) | 87 (0.210) | 55/290 | 12.6 | 30.5% | intergenic (‑53/‑127) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | 5206663 = | 162 (0.390) | intergenic (‑152/‑28) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | = 652785 | 487 (1.160) | 115 (0.320) | 47/256 | 12.6 | 35.3% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4813153 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4813173 | 27 (0.060) | 101 (0.260) | 48/272 | 13.3 | 37.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 310 (0.800) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4813173 | 27 (0.060) | 72 (0.200) | 34/256 | 16.2 | 36.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993954 | 226 (0.620) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 1785057 | 189 (0.450) | 50 (0.130) | 39/282 | 16.2 | 22.2% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | 1785120 = | 170 (0.430) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | = 5993776 | 350 (0.830) | 39 (0.100) | 24/280 | 21.2 | 12.2% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5993968 = | 230 (0.580) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 2300767 = | 328 (0.780) | 11 (0.040) +51 bp |
6/194 | 25.7 | 4.1% | intergenic (+21/+112) | PP_5496/PP_2023 | hypothetical protein/glutathione S‑transferase family protein |
| ? | NC_002947 | 5844566 = | 459 (1.090) | coding (931/993 nt) | yheT | putative hydrolase | |||||
| * | ? | NC_002947 | = 1030245 | 356 (0.850) | 22 (0.060) | 10/242 | 26.1 | 7.3% | intergenic (‑147/+82) | opdP/dppA‑II | glycine‑glutamate dipeptide porin/dipeptide ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 1030284 | 266 (0.780) | intergenic (‑186/+43) | opdP/dppA‑II | glycine‑glutamate dipeptide porin/dipeptide ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 611930 = | NA (NA) | 37 (0.090) | 13/278 | 26.3 | NA | coding (824/966 nt) | PP_0526 | transposase |
| ? | NC_002947 | 611973 = | NA (NA) | coding (867/966 nt) | PP_0526 | transposase | |||||