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 | 1,070,246 | 2 | . | A | 76.5% | 72.7 / 23.1 | 35 | 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 | 1 | . | G | 73.3% | 59.0 / 22.7 | 35 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 55.0% | 20.1 / 175.0 | 130 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 53.3% | ‑3.7 / 16.0 | 30 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 6,000,018 | 0 | C | G | 47.6% | 14.3 / 13.2 | 21 | intergenic (‑172/+28) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 47.4% | ‑0.4 / 13.9 | 22 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 46.0% | 31.6 / 137.1 | 101 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 44.0% | 0.3 / 13.9 | 29 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 41.1% | 82.2 / 126.4 | 108 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 40.0% | 0.3 / 10.7 | 10 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 33.3% | 50.5 / 16.4 | 40 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 3,996,347 | 0 | G | C | 33.3% | 55.7 / 11.2 | 36 | intergenic (+25/+20) | PP_3523/PP_3524 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,044,569 | 0 | A | C | 32.6% | 64.1 / 13.6 | 43 | V380G (GTG→GGG) | PP_3566 | MFS transporter |
| * | NC_002947_CJ‑RC | 1,691,148 | 0 | C | G | 30.4% | 87.5 / 12.7 | 46 | G32G (GGC→GGG) | PP_1487 | hypothetical protein |
| * | NC_002947_CJ‑RC | 2,821,395 | 0 | G | . | 30.4% | 54.0 / 22.1 | 24 | intergenic (‑64/‑327) | PP_2474/PP_2475 | glutathione S‑transferase family protein/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 1,648,938 | 0 | C | A | 29.8% | 99.4 / 10.2 | 48 | intergenic (‑217/+79) | oprB‑II/PP_1446 | carbohydrate‑selective porin/TonB‑dependent receptor |
| * | NC_002947_CJ‑RC | 100,503 | 0 | C | G | 28.6% | 90.8 / 11.6 | 49 | intergenic (‑95/+27) | PP_0094/PP_0095 | 5'‑nucleotidase/hypothetical protein |
| * | NC_002947_CJ‑RC | 3,773,209 | 0 | G | C | 28.6% | 149.0 / 10.1 | 63 | intergenic (+23/‑89) | PP_3333/PP_5743 | hypothetical protein/TonB‑dependent receptor protein |
| * | NC_002947_CJ‑RC | 337,827 | 0 | T | . | 26.3% | 41.0 / 13.6 | 19 | intergenic (‑77/+52) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,140,143 | 0 | G | C | 22.8% | 133.4 / 14.9 | 57 | intergenic (+35/‑230) | PP_3644/PP_5609 | monooxygenase subunit/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 29 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.070) | 22 (0.430) | 12/220 | 4.7 | 50.7% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 39 (0.750) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4635691 | 40 (0.590) | 16 (0.250) | 16/276 | 4.9 | 29.9% | coding (172/639 nt) | uvrY | BarA/UvrY two‑componenent system response regulator |
| ? | NC_002947_CJ‑RC | 4636116 = | 37 (0.570) | coding (200/390 nt) | PP_4100 | Cro/CI family transcriptional regulator | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 62 (0.910) | 15 (0.260) | 12/250 | 5.6 | 36.0% | 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 | = 5684230 | 1 (0.010) | 16 (0.240) +CGGG |
14/282 | 5.7 | 94.3% | 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 | = 5558423 | 3 (0.040) | 13 (0.190) +GCC |
12/284 | 6.4 | 81.6% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.040) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 30 (0.440) | 11 (0.170) | 11/280 | 6.7 | 25.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 36 (0.550) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.090) | 12 (0.190) | 10/266 | 6.8 | 28.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 55 (0.880) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 6 (0.090) | 10 (0.170) | 8/250 | 7.2 | 26.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 50 (0.850) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1156322 = | 11 (0.160) | 8 (0.140) | 6/240 | 8.0 | 40.9% | intergenic (+25/‑191) | PP_1013/yihS | sensor histidine kinase/aldose‑ketose isomerase |
| ? | NC_002947_CJ‑RC | 1156395 = | 14 (0.250) | intergenic (+98/‑118) | PP_1013/yihS | sensor histidine kinase/aldose‑ketose isomerase | |||||
| * | ? | NC_002947_CJ‑RC | = 6016632 | 21 (0.310) | 8 (0.120) +GTGCCC |
6/278 | 9.0 | 30.0% | intergenic (+22/+88) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| ? | NC_002947_CJ‑RC | 6016701 = | 18 (0.260) | intergenic (+91/+19) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein | |||||