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 29 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 | 58.3% | 12.4 / 125.3 | 108 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 52.2% | 9.0 / 27.4 | 23 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 52.2% | ‑4.7 / 13.1 | 24 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 50.0% | 2.0 / 10.0 | 20 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 47.6% | 4.3 / 13.0 | 21 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 44.9% | 45.7 / 38.7 | 91 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 44.8% | 102.8 / 171.8 | 134 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 40.5% | 51.0 / 91.3 | 79 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,544,365 | 0 | T | G | 36.4% | 26.7 / 11.3 | 22 | V390G (GTG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947_CJ‑RC | 441,326 | 0 | G | . | 34.5% | 66.1 / 32.9 | 29 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 33.3% | 47.5 / 11.8 | 47 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,900,594 | 0 | G | C | 33.3% | 22.1 / 10.1 | 15 | intergenic (‑179/+55) | PP_5172/PP_5173 | hypothetical protein/RND family transporter |
| * | NC_002947_CJ‑RC | 6,008,731 | 0 | A | C | 33.3% | 39.2 / 14.3 | 30 | H260P (CAC→CCC) | ydcJ | metalloprotein |
| * | NC_002947_CJ‑RC | 2,584,993 | 0 | A | C | 31.1% | 82.6 / 10.7 | 45 | S168A (TCC→GCC) | folD‑II | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| * | NC_002947_CJ‑RC | 4,798,322 | 0 | A | G | 27.3% | 27.9 / 10.5 | 22 | intergenic (‑177/+41) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 27.1% | 107.4 / 14.3 | 93 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 2,282,775 | 0 | G | C | 26.9% | 34.7 / 17.5 | 26 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,455,911 | 0 | G | T | 26.5% | 98.7 / 12.1 | 49 | intergenic (+109/‑246) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| * | NC_002947_CJ‑RC | 5,449,104 | 0 | T | G | 26.0% | 107.8 / 12.1 | 83 | L145R (CTG→CGG) | thiE | thiamine‑phosphate synthase |
| * | NC_002947_CJ‑RC | 2,192,453 | 0 | G | T | 25.5% | 96.4 / 11.9 | 47 | intergenic (+62/‑142) | PP_1937/PP_1938 | helicase/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 33 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 1 (0.010) | 17 (0.260) | 16/266 | 4.7 | 50.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 33 (0.500) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 57 (0.790) | 17 (0.270) | 14/250 | 4.9 | 40.4% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 1 (0.020) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 8 (0.110) | 11 (0.200) | 8/220 | 6.3 | 33.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 37 (0.680) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 37 (0.510) | 12 (0.170) | 12/280 | 6.3 | 25.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 35 (0.500) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 4 (0.060) | 13 (0.180) +GCC |
12/284 | 6.4 | 76.8% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 4 (0.060) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4586136 | 8 (0.110) | 14 (0.210) | 10/268 | 6.8 | 50.5% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 20 (0.300) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 1 (0.010) | 8 (0.130) | 8/250 | 7.1 | 25.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 45 (0.720) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 401301 | NA (NA) | 6 (0.090) | 6/276 | 8.8 | 12.3% | coding (887/1059 nt) | PP_0334 | transposase |
| ? | NC_002947_CJ‑RC | 401364 = | 45 (0.620) | coding (950/1059 nt) | PP_0334 | transposase | |||||
| * | ? | NC_002947_CJ‑RC | 5916972 = | 20 (0.280) | 4 (0.070) | 4/234 | 8.9 | 19.0% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947_CJ‑RC | 5917068 = | 18 (0.310) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947_CJ‑RC | 2050559 = | 21 (0.290) | 3 (0.060) | 3/216 | 9.1 | 16.9% | intergenic (‑52/+123) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | 2050669 = | 14 (0.260) | intergenic (‑162/+13) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||