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 143 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,813,175 | 0 | A | G | 66.7% | 36.0 / 32.7 | 40 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,813,174 | 0 | A | C | 65.0% | 39.4 / 38.4 | 40 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 4,397,835 | 0 | C | G | 64.3% | ‑5.3 / 11.1 | 14 | R58P (CGG→CCG) | PP_3868 | group II intron‑encoding maturase |
| * | NC_002947 | 4,353,698 | 0 | A | G | 59.3% | 73.5 / inf | 410 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,332,076 | 0 | C | T | 52.3% | 163.7 / inf | 511 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,725 | 0 | A | G | 50.9% | 61.3 / inf | 406 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,813,180 | 0 | C | T | 50.0% | ‑4.9 / 52.7 | 38 | 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 | 50.0% | 4.6 / 53.0 | 38 | intergenic (‑296/‑259) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947 | 1,018,201 | 0 | T | G | 43.3% | 165.8 / 288.8 | 219 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,549,495 | 0 | T | G | 42.3% | 164.6 / inf | 265 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 195,634 | 0 | C | T | 42.2% | 404.7 / inf | 601 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,018,200 | 0 | A | T | 41.2% | 190.5 / 273.9 | 231 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 4,358,197 | 0 | G | C | 41.2% | 81.6 / 23.8 | 69 | T110T (ACG→ACC) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947 | 1,549,492 | 0 | G | C | 40.5% | 245.0 / 315.9 | 248 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 2,287,762 | 0 | T | G | 40.3% | 104.4 / 183.0 | 151 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,345,068 | 0 | A | T | 40.2% | 98.6 / 111.2 | 100 | intergenic (+60/‑271) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,018,194 | 0 | G | C | 39.8% | 260.8 / inf | 246 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 1,018,193 | 0 | G | C | 39.6% | 260.3 / inf | 246 | intergenic (+69/+62) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 4,345,074 | 0 | A | G | 39.3% | 87.5 / 94.0 | 90 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,549,480 | 0 | C | A | 39.0% | 264.1 / 297.3 | 255 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| Marginal new junction evidence (lowest skew 10 of 547 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4813173 | 14 (0.050) | 141 (0.570) | 56/266 | 3.8 | 50.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5993770 = | 261 (1.060) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652785 | 313 (1.170) | 87 (0.380) | 52/250 | 3.8 | 39.2% | 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 | 4813168 = | 42 (0.160) | 84 (0.410) | 43/220 | 4.1 | 43.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993940 | 186 (0.910) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4813173 | 14 (0.050) | 120 (0.520) | 40/250 | 5.4 | 49.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5993954 | 232 (1.000) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 337811 | 155 (0.580) | 80 (0.370) | 36/234 | 5.6 | 38.1% | intergenic (‑58/+71) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| ? | NC_002947 | = 337839 | 135 (0.620) | intergenic (‑86/+43) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease | |||||
| * | ? | NC_002947 | 5482087 = | 167 (0.620) | 44 (0.230) | 26/208 | 6.6 | 28.7% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | 5482186 = | 99 (0.520) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | 5206576 = | 101 (0.380) | 62 (0.310) | 27/216 | 6.7 | 47.0% | intergenic (‑65/‑115) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | 5206671 = | 65 (0.330) | intergenic (‑160/‑20) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | = 5482127 | 156 (0.580) | 68 (0.350) | 24/208 | 7.0 | 39.2% | intergenic (+43/+69) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947 | = 5482144 | 99 (0.520) | intergenic (+60/+52) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947 | 5919162 = | 212 (0.790) | 60 (0.280) | 26/234 | 7.4 | 25.7% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | 5919258 = | 177 (0.820) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | 1119824 = | 212 (0.790) | 52 (0.230) | 27/240 | 7.4 | 23.8% | intergenic (‑64/+115) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947 | 1119900 = | 157 (0.710) | intergenic (‑140/+39) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||