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 80 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_007779 | 438,443 | 1 | . | T | 55.9% | 66.2 / 58.4 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 2 | . | C | 55.9% | 64.6 / 61.3 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 3 | . | G | 55.9% | 67.9 / 58.9 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 4 | . | G | 55.9% | 69.9 / 58.9 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 5 | . | C | 55.9% | 66.1 / 61.3 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 6 | . | A | 55.9% | 72.3 / 58.6 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 7 | . | A | 55.9% | 68.2 / 58.6 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 8 | . | A | 55.9% | 66.4 / 58.6 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 9 | . | C | 55.9% | 67.0 / 61.3 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 10 | . | C | 55.9% | 64.4 / 61.3 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 11 | . | G | 55.9% | 68.0 / 58.9 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 12 | . | C | 55.9% | 66.1 / 61.3 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 13 | . | C | 55.9% | 66.8 / 61.3 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 14 | . | G | 55.9% | 68.7 / 58.9 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 15 | . | C | 55.9% | 66.8 / 61.3 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 16 | . | T | 55.9% | 71.4 / 58.4 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 17 | . | A | 55.9% | 73.1 / 58.6 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 18 | . | C | 55.9% | 70.1 / 61.3 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 19 | . | T | 55.9% | 67.2 / 58.4 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | NC_007779 | 438,443 | 20 | . | T | 55.9% | 66.9 / 58.4 | 34 | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 4310363 = | NA (NA) | 64 (0.560) | 52/496 | 3.2 | 94.1% | intergenic (‑287/‑32) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | = 4540919 | 4 (0.030) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | = 438443 | 1 (0.010) | 55 (0.520) +21 bp |
40/394 | 3.2 | 98.2% | coding (959/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| ? | NC_007779 | 438444 = | 1 (0.010) | coding (958/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase | |||||
| * | ? | NC_007779 | 438444 = | 13 (0.110) | 53 (0.480) | 45/478 | 3.9 | 81.8% | coding (958/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| ? | NC_007779 | = 438464 | 11 (0.100) | coding (938/1863 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase | |||||
| * | ? | NC_007779 | 1413613 = | 130 (1.130) | 18 (0.180) | 17/444 | 9.8 | 14.3% | coding (50/936 nt) | ttcA | tRNA 2‑thiocytidine(32) synthetase TtcA |
| ? | NC_007779 | = 1436672 | 99 (0.960) | intergenic (+39/+227) | Y75_RS24865/uspF | hypothetical protein/universal stress protein UspF | |||||
| * | ? | NC_007779 | = 4547370 | 128 (1.120) | 17 (0.150) | 17/478 | 10.5 | 11.9% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | = 4547666 | 128 (1.160) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 2069490 | 130 (1.130) | 62 (0.540) | 12/496 | 13.0 | 48.1% | intergenic (‑32/+1) | Y75_RS10470/Y75_RS24935 | IS5‑like element IS5 family transposase/hypothetical protein |
| ? | NC_007779 | = 4540919 | 4 (0.030) | intergenic (+208/+375) | Y75_RS22495/Y75_RS22500 | hypothetical protein/9‑O‑acetyl‑N‑acetylneuraminic acid deacetylase | |||||
| * | ? | NC_007779 | 4547362 = | 127 (1.110) | 12 (0.110) | 11/478 | 13.1 | 8.7% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA |
| ? | NC_007779 | 4547676 = | 130 (1.180) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria regulatory protein FimE/metal ABC transporter substrate‑binding lipoprotein/fibrin‑binding adhesin FimA | |||||
| * | ? | NC_007779 | = 2308409 | 86 (0.750) | 3 (0.030) | 3/484 | 18.4 | 3.1% | intergenic (+682/+33) | eco/mqo | serine protease inhibitor ecotin/malate dehydrogenase (quinone) |
| ? | NC_007779 | 2308463 = | 101 (0.900) | coding (1626/1647 nt) | mqo | malate dehydrogenase (quinone) | |||||