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 36 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 | 1,070,246 | 1 | . | G | 71.0% | 57.5 / 27.9 | 32 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 71.0% | 59.2 / 28.7 | 32 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 61.3% | 68.7 / 116.6 | 111 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 58.5% | 14.2 / 143.1 | 123 | 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 | 57.1% | 13.2 / 206.4 | 161 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 52.0% | 7.9 / 27.8 | 26 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 43.5% | 7.6 / 14.0 | 26 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 42.2% | 39.8 / 14.7 | 45 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 5,754,548 | 0 | C | A | 40.7% | 20.2 / 14.6 | 32 | intergenic (‑171/‑300) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 40.3% | 93.2 / 139.5 | 132 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 661,661 | 0 | A | C | 36.4% | 45.4 / 15.1 | 33 | W432G (TGG→GGG) | PP_0569 | MATE efflux family protein |
| * | NC_002947_CJ‑RC | 2,101,751 | 0 | A | C | 31.9% | 39.6 / 13.7 | 49 | L186R (CTG→CGG) | PP_1878 | hypothetical protein |
| * | NC_002947_CJ‑RC | 4,433,580 | 0 | G | C | 31.8% | 68.1 / 20.6 | 44 | intergenic (‑29/‑89) | PP_5648/PP_3928 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,009,108 | 0 | G | T | 31.8% | 120.3 / 18.3 | 64 | S97* (TCG→TAG) | yehW | osmoprotectant ABC transporter permease |
| * | NC_002947_CJ‑RC | 1,531,676 | 0 | T | G | 30.9% | 57.0 / 10.5 | 43 | Q67P (CAG→CCG) | PP_1344 | hypothetical protein |
| * | NC_002947_CJ‑RC | 5,211,931 | 0 | A | G | 30.8% | 52.8 / 13.6 | 40 | intergenic (‑94/+84) | rnd/PP_4592 | ribonuclease D/metal dependent hydrolase |
| * | NC_002947_CJ‑RC | 1,544,365 | 0 | T | G | 30.0% | 65.3 / 20.6 | 40 | V390G (GTG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 28.3% | 50.2 / 11.5 | 49 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 4,001,773 | 0 | T | G | 28.2% | 87.8 / 19.8 | 71 | intergenic (+90/‑44) | dmoA‑II/allE | dimethyl‑sulfide monooxygenase/S‑ureidoglycine aminohydrolase |
| * | NC_002947_CJ‑RC | 1,544,368 | 0 | C | G | 27.5% | 79.0 / 13.9 | 40 | A391G (GCG→GGG) | mdfA | multidrug MFS transporter |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 49 (0.610) | 15 (0.190) | 15/278 | 6.4 | 23.9% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 48 (0.620) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 7 (0.090) | 13 (0.220) | 10/218 | 6.5 | 35.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 42 (0.700) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 14 (0.180) +GCC |
13/282 | 7.2 | 87.7% | 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 | = 5684230 | 1 (0.010) | 18 (0.230) +CGGG |
12/280 | 7.5 | 94.9% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 1 (0.010) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | 1737987 = | 83 (1.040) | 8 (0.110) | 8/254 | 8.6 | 9.2% | coding (32/348 nt) | yffB | glutathione‑dependent thiol reductase |
| ? | NC_002947_CJ‑RC | = 1777401 | 85 (1.210) | intergenic (+135/+157) | PP_5476/PP_1585 | hypothetical protein/antidote protein | |||||
| * | ? | NC_002947_CJ‑RC | 478261 = | 36 (0.450) | 5 (0.080) | 5/228 | 9.4 | 17.4% | intergenic (+9/+101) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase |
| ? | NC_002947_CJ‑RC | 478356 = | 19 (0.300) | intergenic (+104/+6) | PP_0393/cca | 2‑amino‑4‑hydroxy‑6‑ hydroxymethyldihydropteridine pyrophosphokinase/multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 64 (0.800) | 8 (0.130) +29 bp |
3/230 | 10.9 | 21.3% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809865 | 10 (0.130) | intergenic (‑271/‑284) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 5674453 | 36 (0.450) | 3 (0.050) | 3/240 | 11.3 | 10.2% | intergenic (+57/‑113) | PP_4978/PP_4979 | hypothetical protein/substrate‑binding protein |
| ? | NC_002947_CJ‑RC | = 5674490 | 23 (0.350) | intergenic (+94/‑76) | PP_4978/PP_4979 | hypothetical protein/substrate‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 159898 | 79 (0.990) | 4 (0.050) | 4/268 | 11.4 | 5.4% | coding (491/1956 nt) | PP_0149 | hypothetical protein |
| ? | NC_002947_CJ‑RC | = 159912 | 67 (0.900) | coding (477/1956 nt) | PP_0149 | hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4588103 | 56 (0.700) | 4 (0.050) | 4/278 | 11.7 | 7.5% | intergenic (‑182/‑140) | PP_4063/ivd | long‑chain fatty acid‑‑CoA ligase/isovaleryl‑CoA dehydrogenase |
| ? | NC_002947_CJ‑RC | 4588188 = | 45 (0.580) | intergenic (‑267/‑55) | PP_4063/ivd | long‑chain fatty acid‑‑CoA ligase/isovaleryl‑CoA dehydrogenase | |||||