mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 33 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 54.7% | 10.5 / 121.0 | 95 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 699,722 | 0 | A | G | 53.4% | 3.6 / 72.0 | 58 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 52.9% | 4.4 / 133.7 | 104 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,348,705 | 0 | A | G | 41.5% | 52.7 / 94.1 | 82 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 196,879 | 0 | G | A | 35.3% | 17.5 / 10.7 | 17 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 195,559 | 0 | C | A | 31.1% | 129.7 / 77.1 | 90 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 441,326 | 0 | G | . | 25.0% | 54.0 / 17.9 | 24 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947 | 955,155 | 0 | C | T | 24.3% | 55.7 / 18.0 | 39 | intergenic (+109/‑204) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 445,103 | 0 | C | A | 24.1% | 47.7 / 12.3 | 29 | intergenic (+76/‑212) | PP_0367/PP_0368 | hypothetical protein/acyl‑CoA dehydrogenase |
| * | NC_002947 | 196,351 | 0 | C | G | 22.6% | 189.6 / 64.0 | 106 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 955,149 | 0 | A | G | 22.5% | 74.8 / 17.0 | 41 | intergenic (+103/‑210) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 955,152 | 0 | T | A | 22.5% | 66.3 / 16.8 | 41 | intergenic (+106/‑207) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 196,327 | 0 | A | C | 22.1% | 195.4 / 60.3 | 104 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 955,151 | 0 | G | A | 21.9% | 70.2 / 17.2 | 41 | intergenic (+105/‑208) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 955,153 | 0 | T | C | 21.9% | 72.8 / 17.7 | 41 | intergenic (+107/‑206) | cyoE/alaC | protoheme IX farnesyltransferase/aminotransferase |
| * | NC_002947 | 5,740,467 | 0 | T | G | 21.9% | 61.4 / 15.4 | 43 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 2,282,770 | 0 | T | G | 21.6% | 80.9 / 26.3 | 51 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947 | 4,340,089 | 0 | G | C | 20.9% | 71.0 / 13.8 | 44 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,921,549 | 0 | T | A | 20.8% | 86.7 / 20.7 | 48 | intergenic (+24/+37) | PP_1720/PP_1721 | alcohol dehydrogenase/phosphoserine phosphatase |
| * | NC_002947 | 1,921,550 | 0 | T | A | 20.8% | 71.8 / 21.2 | 48 | intergenic (+25/+36) | PP_1720/PP_1721 | alcohol dehydrogenase/phosphoserine phosphatase |
| Marginal new junction evidence (lowest skew 10 of 382 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4808174 = | 11 (0.180) | 18 (0.390) | 12/212 | 3.6 | 40.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988935 | 44 (0.960) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4586029 | 16 (0.260) | 21 (0.370) | 16/260 | 3.6 | 46.8% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586109 | 33 (0.580) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 4808179 | 2 (0.030) | 26 (0.460) | 14/258 | 4.0 | 53.1% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 44 (0.790) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 652782 | 62 (1.010) | 16 (0.300) | 11/242 | 4.6 | 37.6% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808159 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 5870289 | 45 (0.730) | 11 (0.230) | 8/224 | 5.2 | 23.5% | intergenic (+50/+84) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator |
| ? | NC_002947 | = 5870324 | 36 (0.740) | intergenic (+85/+49) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator | |||||
| * | ? | NC_002947 | = 612221 | NA (NA) | 8 (0.180) +36 bp |
6/210 | 5.7 | 11.2% | intergenic (+152/+65) | PP_0526/dxs | transposase/1‑deoxyxylulose‑5‑phosphate synthase |
| ? | NC_002947 | = 2436665 | 85 (1.390) | intergenic (+243/‑416) | PP_2134/fadB | transposase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase | |||||
| * | ? | NC_002947 | 4870666 = | 56 (0.910) | 7 (0.140) | 7/232 | 5.8 | 14.3% | intergenic (+16/‑104) | xdhB/xdhC | xanthine dehydrogenase subunit XdhB/xanthine dehydrogenase accessory factor |
| ? | NC_002947 | 4870736 = | 38 (0.750) | intergenic (+86/‑34) | xdhB/xdhC | xanthine dehydrogenase subunit XdhB/xanthine dehydrogenase accessory factor | |||||
| * | ? | NC_002947 | = 1780066 | 27 (0.440) | 9 (0.150) | 9/268 | 5.8 | 24.1% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | 1780129 = | 31 (0.530) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | = 2957080 | 65 (1.060) | 9 (0.150) | 9/272 | 5.9 | 12.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947 | 2957165 = | 65 (1.100) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947 | = 1917232 | 48 (0.780) | 8 (0.140) | 8/260 | 6.0 | 14.9% | coding (993/1083 nt) | PP_1718 | EAL domain‑containing diguanylate phosphodiesterase |
| ? | NC_002947 | = 1917289 | 47 (0.830) | coding (936/1083 nt) | PP_1718 | EAL domain‑containing diguanylate phosphodiesterase | |||||