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 45 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 | 697,094 | 0 | A | G | 66.7% | 6.7 / 11.3 | 24 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 61.9% | ‑4.0 / 11.6 | 22 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 59.3% | ‑6.3 / 16.7 | 29 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,842,800 | 0 | T | G | 52.4% | 1.7 / 19.1 | 22 | Q665P (CAG→CCG) | gacS | sensor protein GacS |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 50.4% | 32.8 / 195.7 | 135 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 50.3% | ‑5.3 / 212.0 | 147 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 50.0% | 3.7 / 10.4 | 24 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 49.1% | 88.5 / 253.4 | 177 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 46.7% | 3.3 / 10.9 | 30 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,842,816 | 0 | T | C | 45.0% | 5.2 / 10.7 | 21 | S660G (AGC→GGC) | gacS | sensor protein GacS |
| * | NC_002947_CJ‑RC | 5,462,375 | 0 | T | G | 40.5% | 22.6 / 11.5 | 42 | intergenic (+18/‑22) | PP_4795/holA | lipoprotein/DNA polymerase III subunit delta |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 39.5% | 23.7 / 12.3 | 48 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 36.2% | 33.6 / 18.3 | 48 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 4,935,572 | 0 | A | C | 35.5% | 53.4 / 17.6 | 64 | W194G (TGG→GGG) | flhF | flagellar biosynthesis protein FlhF |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 34.0% | 33.2 / 10.8 | 48 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 4,844,607 | 1 | . | G | 33.3% | 20.7 / 32.3 | 21 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947_CJ‑RC | 3,076,087 | 0 | G | T | 32.3% | 25.9 / 14.8 | 36 | intergenic (‑35/+39) | PP_2685/PP_2686 | hypothetical protein/transglutaminase domain‑containing protein |
| * | NC_002947_CJ‑RC | 4,648,341 | 0 | A | C | 29.6% | 86.6 / 10.6 | 54 | V302G (GTG→GGG) | PP_4112 | sulfate transporter |
| * | NC_002947_CJ‑RC | 3,989,361 | 0 | A | C | 29.6% | 136.8 / 16.2 | 71 | T627P (ACC→CCC) | oplA | 5‑oxoprolinase A |
| * | NC_002947_CJ‑RC | 2,171,499 | 0 | T | G | 29.0% | 114.6 / 11.0 | 65 | intergenic (+34/+369) | PP_5484/PP_1924 | hypothetical protein/phosphinothricin N‑acetyltransferase |
| Marginal new junction evidence (lowest skew 10 of 41 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 1 (0.010) | 24 (0.280) | 17/266 | 7.0 | 48.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 51 (0.600) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 31 (0.330) | 19 (0.210) | 18/280 | 7.1 | 31.4% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 53 (0.590) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.050) | 17 (0.240) | 12/220 | 7.2 | 33.7% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 63 (0.890) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 17 (0.190) +GCC |
13/284 | 9.1 | 94.5% | 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 | = 1780066 | 14 (0.150) | 13 (0.150) | 12/276 | 9.2 | 41.7% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 23 (0.260) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | 4647664 = | 30 (0.320) | 5 (0.070) | 5/212 | 10.7 | 17.0% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | 4647772 = | 27 (0.400) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 5 (0.050) | 7 (0.090) | 6/238 | 11.0 | 20.9% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991594 = | 49 (0.640) | intergenic (+73/‑473) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2050595 | 23 (0.250) | 4 (0.060) | 4/216 | 11.6 | 14.5% | intergenic (‑88/+87) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 2050631 | 30 (0.430) | intergenic (‑124/+51) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 58 (0.620) | 7 (0.080) | 7/274 | 11.7 | 9.2% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 83 (0.940) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5384135 | 28 (0.300) | 4 (0.060) | 4/220 | 11.7 | 19.4% | intergenic (+52/+81) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947_CJ‑RC | = 5384163 | 12 (0.170) | intergenic (+80/+53) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||