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 35 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 | 4,158,471 | 0 | A | C | 55.2% | ‑1.8 / 20.8 | 31 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 54.3% | 34.1 / 241.2 | 175 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 53.3% | 12.6 / 161.1 | 122 | 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 | 50.0% | 10.3 / 219.0 | 145 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,174,938 | 0 | G | C | 50.0% | 32.9 / 15.7 | 38 | intergenic (‑276/+56) | fadD‑I/fadD‑II | long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 45.2% | 10.2 / 10.2 | 31 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 45.0% | 9.2 / 10.4 | 26 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,174,935 | 0 | C | A | 44.7% | 35.5 / 18.8 | 38 | intergenic (‑273/+59) | fadD‑I/fadD‑II | long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 44.2% | 76.7 / 180.1 | 149 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 34.7% | 51.4 / 11.3 | 51 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 32.7% | 172.6 / 85.1 | 105 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 31.2% | 17.3 / 13.7 | 16 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 4,740,951 | 0 | C | G | 30.0% | 31.5 / 14.1 | 20 | intergenic (+81/+672) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947_CJ‑RC | 5,743,285 | 0 | A | T | 29.4% | 16.7 / 10.1 | 17 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 798,664 | 0 | T | G | 28.6% | 44.0 / 11.0 | 36 | intergenic (+19/+8) | fklB‑I/PP_0685 | FKBP‑type peptidyl‑prolyl cis‑trans isomerase/hypothetical protein |
| * | NC_002947_CJ‑RC | 1,544,504 | 0 | T | G | 27.8% | 33.7 / 10.7 | 18 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 5,743,282 | 0 | T | G | 27.8% | 17.0 / 13.7 | 18 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 4,524,632 | 0 | G | T | 26.6% | 143.3 / 11.3 | 66 | intergenic (+148/‑45) | idh/PP_4013 | isocitrate dehydrogenase/MutT/nudix family protein |
| * | NC_002947_CJ‑RC | 4,356,312 | 0 | C | G | 26.3% | 139.8 / 10.8 | 59 | F241L (TTC→TTG) | modC | molybdate ABC transporter ATP‑binding protein ModC |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 25.8% | 215.6 / 98.6 | 124 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 32 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 6 (0.070) | 29 (0.450) | 19/222 | 4.1 | 56.6% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 40 (0.620) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 40 (0.470) | 28 (0.340) | 26/282 | 4.1 | 42.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 38 (0.460) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 21 (0.250) | 16 (0.200) | 16/278 | 6.7 | 45.1% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 19 (0.240) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 652782 | 61 (0.720) | 14 (0.190) | 12/252 | 7.4 | 34.3% | 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 | = 5558423 | 1 (0.010) | 16 (0.190) +GCC |
13/286 | 8.0 | 94.2% | 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 | = 5684230 | 4 (0.050) | 14 (0.170) +CGGG |
11/284 | 8.8 | 78.3% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 4 (0.050) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 12 (0.140) | 10 (0.140) | 8/252 | 9.2 | 23.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 56 (0.760) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 40 (0.470) | 9 (0.110) | 9/278 | 9.6 | 13.2% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 80 (0.990) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | 4647664 = | 33 (0.390) | 3 (0.050) | 3/214 | 11.1 | 13.0% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947_CJ‑RC | 4647772 = | 16 (0.260) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 74 (0.870) | 7 (0.090) | 6/276 | 11.2 | 9.9% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 57 (0.710) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||