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 25 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 | 699,722 | 0 | A | G | 57.1% | 29.6 / 145.1 | 119 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,107 | 0 | T | G | 56.2% | ‑1.7 / 11.8 | 20 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,712,093 | 0 | T | A | 55.6% | 9.3 / 18.5 | 19 | intergenic (+84/‑174) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 54.6% | 2.0 / 140.0 | 108 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 53.1% | 45.7 / 207.5 | 147 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 52.4% | ‑2.1 / 20.6 | 23 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 50.4% | 29.3 / 211.0 | 137 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 37.2% | 18.6 / 10.9 | 43 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 36.0% | 134.9 / 89.6 | 89 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,512,723 | 0 | T | G | 34.0% | 38.7 / 11.3 | 47 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 2,282,774 | 0 | G | C | 33.3% | 19.7 / 24.6 | 24 | intergenic (‑166/+63) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,282,775 | 0 | G | C | 33.3% | 23.7 / 24.2 | 24 | intergenic (‑167/+62) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 3,207,678 | 0 | A | C | 32.6% | 84.8 / 10.9 | 49 | S443R (AGC→CGC) | PP_2812 | transporter |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 32.0% | 20.5 / 25.8 | 25 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,754,548 | 0 | C | A | 32.0% | 44.4 / 12.1 | 28 | intergenic (‑171/‑300) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 30.6% | 76.0 / 14.4 | 50 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 3,312,690 | 0 | A | T | 27.8% | 39.0 / 10.3 | 37 | intergenic (+31/‑131) | PP_2912/hemB | hypothetical protein/5‑aminolevulinate dehydratase |
| * | NC_002947_CJ‑RC | 2,282,779 | 0 | C | A | 27.6% | 51.6 / 20.7 | 29 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 24.6% | 85.2 / 11.0 | 66 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 1,007,524 | 0 | G | T | 24.3% | 63.0 / 11.2 | 37 | intergenic (+24/+66) | PP_0867/yehX | FecA‑like outer membrane receptor/ABC transporter ATP‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 36 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 13 (0.180) | 16 (0.230) | 16/278 | 4.5 | 53.9% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 15 (0.220) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 39 (0.530) | 16 (0.230) | 16/282 | 4.6 | 27.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 48 (0.680) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 18 (0.250) +GCC |
14/286 | 5.2 | 100% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 0 (0.000) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 53 (0.720) | 15 (0.240) | 11/252 | 5.4 | 39.6% | 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 | = 5991586 | 50 (0.680) | 10 (0.140) | 10/276 | 6.3 | 14.9% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 67 (0.970) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 9 (0.130) | 7/268 | 7.4 | 25.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 50 (0.740) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 10 (0.160) | 6/252 | 7.5 | 24.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 58 (0.920) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1737987 = | 94 (1.280) | 6 (0.090) | 6/258 | 7.6 | 6.9% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
| ? | NC_002947_CJ‑RC | = 1777401 | 79 (1.220) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5290102 | 25 (0.340) | 7 (0.100) | 6/274 | 8.0 | 15.0% | intergenic (‑80/+104) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290245 = | 56 (0.810) | coding (633/672 nt) | mdaB | drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | = 2282748 | 20 (0.270) | 6 (0.090) | 6/280 | 8.1 | 21.8% | intergenic (‑140/+89) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| ? | NC_002947_CJ‑RC | 2282815 = | 24 (0.340) | intergenic (‑207/+22) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein | |||||