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 41 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 | 5,558,423 | 2 | . | C | 93.8% | 48.0 / ‑3.0 | 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 93.8% | 48.0 / ‑3.0 | 16 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 62.1% | 44.4 / 37.9 | 31 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 62.1% | ‑5.1 / 15.6 | 30 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 60.0% | ‑1.1 / 15.0 | 21 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 59.3% | 40.3 / 37.5 | 31 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 55.6% | ‑3.2 / 18.8 | 31 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 697,112 | 0 | G | C | 55.0% | 3.2 / 21.5 | 20 | intergenic (+39/‑712) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,712,075 | 0 | G | T | 53.3% | 7.4 / 20.1 | 15 | intergenic (+66/‑192) | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 53.3% | 11.3 / 181.5 | 137 | 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 | 52.5% | 55.8 / 232.2 | 162 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,844,599 | 0 | C | . | 44.4% | 12.4 / 11.0 | 9 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947_CJ‑RC | 4,844,607 | 1 | . | G | 44.4% | 9.1 / 16.6 | 9 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 41.5% | 79.1 / 154.8 | 130 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 40.7% | 38.4 / 17.6 | 58 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 3,323,600 | 0 | C | G | 40.0% | 24.2 / 10.2 | 30 | R98P (CGC→CCC) | PP_2923 | hypothetical protein |
| * | NC_002947_CJ‑RC | 1,013,249 | 0 | T | G | 37.5% | 15.8 / 18.1 | 16 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 36.4% | 23.8 / 15.6 | 60 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 4,740,946 | 0 | C | G | 36.4% | 18.3 / 18.8 | 22 | intergenic (+76/+677) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 1,013,248 | 0 | A | T | 31.6% | 27.3 / 10.6 | 19 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 43 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 4 (0.050) | 17 (0.270) | 13/222 | 5.7 | 47.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 34 (0.530) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 34 (0.410) | 20 (0.250) | 18/282 | 5.8 | 32.0% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 52 (0.640) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 14 (0.180) | 12/268 | 7.4 | 33.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 53 (0.690) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 74 (0.880) | 13 (0.180) | 10/252 | 7.8 | 29.0% | 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 | = 1419549 | 24 (0.290) | 14 (0.170) | 12/286 | 8.0 | 33.9% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 31 (0.380) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 7 (0.080) | 11 (0.130) +GCC |
11/286 | 8.4 | 61.6% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 7 (0.080) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 9 (0.120) | 8/252 | 8.8 | 27.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 44 (0.610) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 16 (0.190) | 17 (0.210) +CT |
9/288 | 9.3 | 44.5% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1780139 | 27 (0.320) | intergenic (+98/+8) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 278744 | 24 (0.290) | 11 (0.140) | 8/270 | 9.3 | 27.8% | intergenic (‑239/+75) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| ? | NC_002947_CJ‑RC | = 278792 | 35 (0.450) | intergenic (‑287/+27) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 15 (0.180) | 8 (0.100) | 8/278 | 9.5 | 31.8% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 20 (0.250) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||