mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.2 revision caddc01d3be9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 66 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,741,275 | 0 | A | G | 69.0% | 112.6 / 56.5 | 85 | intergenic (+466/+286) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,273 | 1 | . | C | 68.2% | 196.4 / 92.0 | 85 | intergenic (+464/+288) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 699,725 | 0 | A | G | 57.6% | 59.3 / 150.0 | 133 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,741,299 | 0 | C | T | 53.7% | ‑0.7 / 123.4 | 95 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | C | 53.7% | 145.5 / 181.3 | 95 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 52.6% | 2.9 / 128.7 | 95 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 52.6% | 8.9 / 150.8 | 95 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,348,749 | 0 | A | G | 52.2% | ‑0.4 / 270.6 | 205 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 51.1% | 55.0 / 239.1 | 175 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,842,941 | 0 | C | . | 47.8% | 192.4 / 227.6 | 115 | intergenic (+40/‑257) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 4,842,949 | 1 | . | G | 47.3% | 29.2 / 259.7 | 112 | intergenic (+48/‑249) | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | NC_002947 | 4,741,298 | 1 | . | T | 46.3% | 155.4 / 212.1 | 95 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 46.3% | 1.0 / 121.3 | 95 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 5,655,687 | 0 | C | A | 40.5% | 83.5 / 96.4 | 89 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 5,655,692 | 0 | T | . | 39.5% | 159.9 / 120.7 | 81 | intergenic (‑96/+56) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 195,634 | 0 | C | T | 38.8% | 218.2 / 269.4 | 266 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,655,682 | 0 | T | G | 36.6% | 85.0 / 101.4 | 93 | intergenic (‑86/+66) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 4,049,951 | 0 | A | G | 35.1% | 99.3 / 83.9 | 94 | intergenic (+40/‑61) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| * | NC_002947 | 4,049,954 | 0 | C | G | 35.1% | 122.3 / 99.7 | 94 | intergenic (+43/‑58) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| * | NC_002947 | 4,049,957 | 0 | C | T | 35.1% | 102.0 / 84.3 | 94 | intergenic (+46/‑55) | quiA/oprB‑III | quinate dehydrogenase/carbohydrate‑selective porin |
| Marginal new junction evidence (lowest skew 10 of 765 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4586100 | 71 (0.490) | 49 (0.470) | 33/190 | 3.4 | 51.1% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 43 (0.410) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 652785 | 102 (0.700) | 57 (0.460) | 39/226 | 3.6 | 56.8% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808204 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4808224 | 0 (0.000) | 64 (0.480) | 34/242 | 4.9 | 45.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988821 = | 153 (1.160) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 6013891 | 64 (0.440) | 36 (0.310) | 23/212 | 6.2 | 40.9% | intergenic (+40/+70) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| ? | NC_002947 | = 6013919 | 53 (0.460) | intergenic (+68/+42) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein | |||||
| * | ? | NC_002947 | = 4808224 | 0 (0.000) | 53 (0.430) | 24/226 | 6.5 | 48.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5989005 | 112 (0.910) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 337811 | 107 (0.740) | 38 (0.330) | 21/210 | 6.7 | 33.9% | intergenic (‑58/+71) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| ? | NC_002947 | = 337839 | 64 (0.560) | intergenic (‑86/+43) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease | |||||
| * | ? | NC_002947 | = 5453186 | 10 (0.070) | 25 (0.270) +48 bp |
15/170 | 6.9 | 47.9% | intergenic (+151/‑204) | lnt/PP_4791 | apolipoprotein N‑acyltransferase/transposase |
| ? | NC_002947 | 5545674 = | 75 (0.520) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 5224548 = | 9 (0.060) | 25 (0.270) +48 bp |
15/170 | 6.9 | 48.2% | intergenic (‑204/+175) | PP_4603/PP_4604 | transposase/DMT superfamily permease |
| ? | NC_002947 | 5545674 = | 75 (0.520) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | = 5201663 | 94 (0.650) | 29 (0.280) | 18/192 | 6.9 | 33.6% | intergenic (‑101/‑79) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | = 5201684 | 47 (0.450) | intergenic (‑122/‑58) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | 4075662 = | 4 (0.030) | 25 (0.270) +48 bp |
15/170 | 6.9 | 49.8% | intergenic (‑204/+237) | PP_3586/tpx | transposase/2‑Cys peroxiredoxin |
| ? | NC_002947 | 5545674 = | 75 (0.520) | intergenic (‑766/+111) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||