mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 27 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 | 72.2% | 73.2 / 31.6 | 36 | 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 | 71.4% | 75.8 / 32.4 | 36 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 4,530,125 | 0 | C | A | 53.8% | 5.9 / 13.7 | 14 | intergenic (+24/‑144) | PP_4018/topB | acetyltransferase/DNA topoisomerase III |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 52.7% | 19.4 / 105.4 | 74 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,544,404 | 0 | T | G | 52.6% | ‑1.3 / 22.3 | 19 | V403G (GTG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947_CJ‑RC | 3,466,841 | 0 | T | G | 52.0% | ‑0.5 / 18.0 | 26 | intergenic (‑16/+108) | PP_3081/PP_5560 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 5,226,245 | 0 | C | A | 46.2% | 19.9 / 11.8 | 27 | intergenic (‑246/+133) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 45.8% | 62.6 / 181.1 | 132 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 44.4% | 37.2 / 22.0 | 68 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 43.6% | 21.7 / 68.0 | 56 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,615,455 | 0 | G | T | 42.4% | 17.2 / 11.4 | 33 | intergenic (+18/‑211) | PP_3186/codB | transcriptional regulator/cytosine transporter |
| * | NC_002947_CJ‑RC | 6,000,018 | 0 | C | G | 41.2% | 42.0 / 11.8 | 35 | intergenic (‑172/+28) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 36.4% | 44.4 / 16.9 | 57 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,773,949 | 0 | T | G | 34.8% | 114.8 / 17.0 | 68 | E610A (GAG→GCG) | betT‑I | choline transporter |
| * | NC_002947_CJ‑RC | 5,560,715 | 0 | C | A | 34.6% | 41.4 / 10.9 | 26 | intergenic (‑271/+60) | PP_4888/purA | methyl‑accepting chemotaxis transducer/adenylosuccinate synthetase |
| * | NC_002947_CJ‑RC | 4,442,726 | 0 | A | C | 32.7% | 59.2 / 12.8 | 59 | intergenic (‑89/+49) | nicP‑II/nicT | porin‑like protein/metabolite transport protein NicT |
| * | NC_002947_CJ‑RC | 6,007,802 | 0 | T | G | 27.0% | 46.6 / 12.1 | 39 | intergenic (+25/‑151) | PP_5259/ydcJ | LysR family transcriptional regulator/metalloprotein |
| * | NC_002947_CJ‑RC | 3,280,860 | 0 | G | T | 25.3% | 189.0 / 13.7 | 79 | E48* (GAA→TAA) | PP_2881 | short‑chain dehydrogenase/reductase family oxidoreductase |
| * | NC_002947_CJ‑RC | 3,076,087 | 0 | G | T | 25.0% | 38.6 / 11.2 | 39 | intergenic (‑35/+39) | PP_2685/PP_2686 | hypothetical protein/transglutaminase domain‑containing protein |
| * | NC_002947_CJ‑RC | 4,935,577 | 0 | T | G | 24.7% | 126.7 / 14.8 | 84 | Q192P (CAG→CCG) | flhF | flagellar biosynthesis protein FlhF |
| Marginal new junction evidence (lowest skew 10 of 32 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 53 (0.660) | 26 (0.340) | 23/276 | 3.2 | 35.4% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 45 (0.590) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 46 (0.570) | 19 (0.240) | 19/282 | 4.1 | 26.7% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 60 (0.770) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 18 (0.230) +GCC |
17/286 | 4.6 | 94.8% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 1 (0.010) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 4 (0.050) | 11 (0.180) | 10/222 | 5.3 | 34.4% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 39 (0.630) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991572 | 59 (0.730) | 10 (0.130) | 9/276 | 6.8 | 15.9% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991794 = | 50 (0.650) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 18 (0.220) | 9 (0.120) | 9/278 | 6.9 | 31.0% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 23 (0.300) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 57 (0.710) | 7 (0.100) | 7/252 | 7.1 | 22.1% | 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 | = 2282748 | 14 (0.170) | 8 (0.100) | 8/280 | 7.3 | 28.9% | intergenic (‑140/+89) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| ? | NC_002947_CJ‑RC | 2282815 = | 26 (0.340) | intergenic (‑207/+22) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 3 (0.040) | 12 (0.150) +CGGG |
8/284 | 7.4 | 80.4% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 3 (0.040) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 0 (0.000) | 8 (0.110) | 6/268 | 8.0 | 24.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 50 (0.670) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||