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 30 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 54.2% | 4.4 / 169.2 | 131 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 51.1% | ‑5.4 / 129.3 | 94 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 42.3% | 13.9 / 16.4 | 31 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 42.3% | 123.0 / 153.9 | 130 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 41.4% | 83.8 / 128.1 | 117 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 33.7% | 103.3 / 83.7 | 92 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 30.6% | 138.7 / 60.1 | 74 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 30.0% | 66.2 / 12.0 | 50 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 697,138 | 0 | C | G | 29.6% | 41.3 / 11.8 | 29 | intergenic (+65/‑686) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 27.0% | 213.5 / 114.4 | 126 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,340,190 | 0 | A | G | 26.1% | 34.4 / 10.8 | 23 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947_CJ‑RC | 4,340,191 | 0 | C | T | 26.1% | 39.3 / 10.2 | 23 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947_CJ‑RC | 4,798,317 | 0 | G | C | 25.9% | 42.5 / 16.7 | 27 | intergenic (‑172/+46) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 25.8% | 50.5 / 15.4 | 32 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,703,248 | 0 | A | G | 25.0% | 34.7 / 10.6 | 24 | intergenic (+97/‑70) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 1,703,252 | 0 | C | T | 25.0% | 38.1 / 10.2 | 25 | intergenic (+101/‑66) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 5,658,441 | 1 | . | A | 25.0% | 36.8 / 14.6 | 16 | intergenic (‑81/+71) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947_CJ‑RC | 2,051,062 | 0 | G | C | 24.7% | 189.4 / 16.2 | 77 | intergenic (‑60/+26) | PP_1825/PP_1826 | hypothetical protein/isochorismatase family hydrolase |
| * | NC_002947_CJ‑RC | 1,703,250 | 0 | G | C | 24.0% | 48.3 / 14.5 | 25 | intergenic (+99/‑68) | lysS/PP_1497 | lysine‑‑tRNA ligase/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 5,392,150 | 0 | G | T | 24.0% | 124.7 / 14.1 | 50 | intergenic (+536/‑186) | PP_4738/PP_mr56 | hypothetical protein/C4 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 47 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 23 (0.290) +GCC |
18/282 | 5.7 | 92.2% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 6 (0.080) | 15 (0.250) | 11/218 | 6.1 | 40.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 39 (0.640) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 42 (0.530) | 16 (0.210) | 15/278 | 6.5 | 24.5% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 58 (0.750) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 74 (0.930) | 12 (0.170) | 11/248 | 7.1 | 27.4% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 7 (0.090) | 13 (0.180) | 12/264 | 7.2 | 28.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 58 (0.790) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 14 (0.180) | 11 (0.140) | 11/274 | 7.8 | 37.1% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 24 (0.320) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 7 (0.090) | 8 (0.120) | 8/248 | 8.4 | 22.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 48 (0.700) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1737987 = | 88 (1.100) | 7 (0.100) | 7/254 | 9.2 | 8.4% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
| ? | NC_002947_CJ‑RC | = 1777401 | 75 (1.060) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2282748 | 25 (0.310) | 9 (0.120) | 8/276 | 9.3 | 28.6% | intergenic (‑140/+89) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| ? | NC_002947_CJ‑RC | 2282815 = | 21 (0.270) | intergenic (‑207/+22) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 2 (0.030) | 9 (0.120) +CGGG |
8/280 | 9.4 | 82.2% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 2 (0.030) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||