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 29 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 | 4,530,125 | 0 | C | A | 54.5% | 3.0 / 11.9 | 11 | intergenic (+24/‑144) | PP_4018/topB | acetyltransferase/DNA topoisomerase III |
| * | NC_002947_CJ‑RC | 5,164,212 | 0 | G | T | 51.2% | 47.3 / 67.5 | 44 | intergenic (+32/+169) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 5,455,911 | 0 | G | T | 50.0% | 9.7 / 11.2 | 21 | intergenic (+109/‑246) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 46.7% | 51.0 / 148.6 | 105 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 5,164,233 | 0 | G | T | 44.7% | 41.6 / 14.1 | 38 | intergenic (+53/+148) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 697,097 | 0 | C | G | 44.4% | 2.7 / 10.9 | 18 | intergenic (+24/‑727) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 43.5% | 119.7 / 180.7 | 147 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 43.0% | 36.1 / 97.5 | 79 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 40.6% | 108.7 / 147.7 | 135 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,170,180 | 0 | T | G | 40.0% | ‑1.9 / 10.8 | 10 | intergenic (‑288/‑99) | katG/PP_3669 | catalase‑peroxidase/LysR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 2,821,395 | 0 | G | . | 37.5% | 31.2 / 18.6 | 17 | intergenic (‑64/‑327) | PP_2474/PP_2475 | glutathione S‑transferase family protein/TetR family transcriptional regulator |
| * | NC_002947_CJ‑RC | 5,164,207 | 0 | A | C | 37.0% | 69.6 / 15.9 | 52 | intergenic (+27/+174) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 5,164,209 | 0 | C | G | 36.0% | 82.0 / 13.6 | 51 | intergenic (+29/+172) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 5,226,245 | 0 | C | A | 32.4% | 78.1 / 14.7 | 37 | intergenic (‑246/+133) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| * | NC_002947_CJ‑RC | 5,164,220 | 0 | G | C | 31.9% | 73.2 / 15.2 | 48 | intergenic (+40/+161) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 5,164,215 | 0 | A | C | 30.4% | 70.6 / 15.9 | 46 | intergenic (+35/+166) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947_CJ‑RC | 5,834,696 | 0 | A | C | 30.4% | 86.6 / 11.2 | 46 | V88G (GTA→GGA) | ftsY | signal recognition particle protein translocation receptor GTPase |
| * | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 28.6% | 39.9 / 16.2 | 28 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 2,282,779 | 0 | C | A | 28.6% | 56.7 / 19.5 | 28 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 24.3% | 310.2 / 119.3 | 148 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 652782 | 53 (0.670) | 24 (0.350) | 20/234 | 3.1 | 51.5% | 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 | = 4809882 | 3 (0.040) | 18 (0.250) | 17/250 | 4.0 | 35.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 63 (0.870) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 11 (0.140) | 16 (0.270) | 12/204 | 4.2 | 35.5% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 50 (0.850) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 13 (0.190) | 13/234 | 4.6 | 26.9% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 68 (1.010) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 15 (0.190) +GCC |
14/268 | 5.0 | 100% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 0 (0.000) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5384135 | 69 (0.870) | 6 (0.100) | 5/204 | 6.8 | 11.7% | intergenic (+52/+81) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947_CJ‑RC | = 5384163 | 39 (0.660) | intergenic (+80/+53) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947_CJ‑RC | = 2050595 | 18 (0.230) | 4 (0.070) | 4/200 | 7.2 | 21.6% | intergenic (‑88/+87) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 2050631 | 16 (0.280) | intergenic (‑124/+51) | PP_1824/PP_1825 | Smr domain‑containing protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5290126 | 71 (0.900) | 4 (0.060) | 4/214 | 7.6 | 5.8% | intergenic (‑104/+80) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | = 5290160 | 74 (1.200) | intergenic (‑138/+46) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | 330227 = | 87 (1.100) | 4 (0.050) | 4/256 | 8.5 | 5.0% | coding (117/2298 nt) | PP_0272 | ferric siderophore receptor |
| ? | NC_002947_CJ‑RC | 5549368 = | 71 (0.960) | coding (2501/2574 nt) | rnr | exoribonuclease R | |||||
| * | ? | NC_002947_CJ‑RC | = 2064021 | 63 (0.790) | 4 (0.050) | 4/272 | 8.8 | 5.7% | coding (258/333 nt) | PP_1840 | hypothetical protein |
| ? | NC_002947_CJ‑RC | 5428125 = | 69 (0.880) | coding (909/915 nt) | PP_4764 | histone deacetylase family protein | |||||