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 | 278,742 | 1 | . | A | 71.9% | 71.0 / 29.5 | 32 | intergenic (‑237/+77) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 63.3% | 4.7 / 21.7 | 31 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,107 | 0 | T | G | 60.0% | 3.0 / 24.0 | 29 | intergenic (+34/‑717) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 59.3% | ‑5.2 / 17.6 | 28 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 52.8% | 46.0 / 250.8 | 176 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 51.3% | 7.7 / 31.0 | 38 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 51.2% | 1.1 / 29.0 | 45 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 47.1% | 10.5 / 14.2 | 37 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 46.7% | 16.6 / 17.3 | 48 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 45.5% | ‑2.6 / 12.3 | 11 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 4,809,884 | 0 | A | G | 45.5% | ‑2.1 / 10.2 | 11 | intergenic (‑290/‑265) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 43.3% | 53.4 / 118.5 | 98 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,842,816 | 0 | T | C | 42.9% | 15.9 / 14.5 | 29 | S660G (AGC→GGC) | gacS | sensor protein GacS |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 41.4% | 11.1 / 17.6 | 29 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 40.8% | 95.5 / 142.1 | 120 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 697,123 | 0 | G | T | 38.2% | 31.6 / 18.8 | 34 | intergenic (+50/‑701) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,097 | 0 | C | G | 37.5% | 26.8 / 12.4 | 32 | intergenic (+24/‑727) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,798,322 | 0 | A | G | 36.8% | 14.4 / 11.9 | 21 | intergenic (‑177/+41) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 36.6% | 20.5 / 14.7 | 41 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 697,138 | 0 | C | G | 34.2% | 63.4 / 11.3 | 38 | intergenic (+65/‑686) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| Marginal new junction evidence (lowest skew 10 of 46 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 4274080 | 0 (0.000) | 17 (0.380) +61 bp |
11/170 | 4.2 | 70.1% | intergenic (‑204/‑71) | glcC/glcD | transcriptional regulator GlcC/glycolate oxidase FAD‑linked subunit |
| ? | NC_002947_CJ‑RC | 4768013 = | 25 (0.320) | intergenic (+120/‑62) | fpvA/tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein | |||||
| * | ? | NC_002947_CJ‑RC | 4768013 = | 17 (0.220) | 28 (0.360) | 21/290 | 4.7 | 36.4% | intergenic (+120/‑62) | fpvA/tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein |
| ? | NC_002947_CJ‑RC | 5398523 = | 81 (1.040) | intergenic (‑69/‑67) | tphA2II/hsdM | terephthalate 1,2‑dioxygenase subunit alpha/type I restriction modification system methylase | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 12 (0.150) | 17 (0.290) | 11/222 | 5.9 | 36.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 49 (0.830) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4274080 | 0 (0.000) | 11 (0.250) +62 bp |
6/166 | 6.2 | 33.7% | intergenic (‑204/‑71) | glcC/glcD | transcriptional regulator GlcC/glycolate oxidase FAD‑linked subunit |
| ? | NC_002947_CJ‑RC | = 5398515 | 76 (0.980) | intergenic (‑61/‑75) | tphA2II/hsdM | terephthalate 1,2‑dioxygenase subunit alpha/type I restriction modification system methylase | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 53 (0.680) | 13 (0.190) | 12/252 | 6.4 | 35.8% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 1 (0.010) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 7 (0.090) | 14 (0.200) | 13/268 | 6.5 | 32.8% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 51 (0.710) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 49 (0.630) | 13 (0.170) | 13/282 | 6.9 | 21.6% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 47 (0.620) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4647702 | 26 (0.330) | 8 (0.140) | 7/214 | 7.4 | 29.1% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | = 4647732 | 20 (0.350) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 3 (0.040) | 9 (0.120) +GCC |
9/286 | 8.6 | 75.4% | 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 | = 2837075 | 16 (0.200) | 6 (0.080) | 6/268 | 9.7 | 29.5% | intergenic (‑27/+156) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947_CJ‑RC | 2837172 = | 14 (0.200) | intergenic (‑124/+59) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||