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 30 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,722 | 0 | A | G | 64.1% | 53.6 / 70.5 | 79 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 51.1% | 11.0 / 121.6 | 90 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,121 | 0 | C | T | 47.9% | 55.7 / 161.1 | 124 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 41.8% | 84.7 / 121.0 | 110 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 2,038,351 | 0 | G | . | 38.5% | 21.9 / 14.1 | 13 | coding (1129/1143 nt) | rffE | UDP‑N‑acetylglucosamine‑2‑epimerase |
| * | NC_002947 | 197,590 | 0 | T | C | 30.3% | 119.0 / 67.4 | 89 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 197,572 | 0 | G | A | 27.5% | 140.5 / 62.6 | 91 | K1026K (AAG→AAA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,089 | 0 | G | C | 26.7% | 51.3 / 14.9 | 31 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 195,559 | 0 | C | A | 26.6% | 151.4 / 52.3 | 80 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,083 | 0 | A | G | 25.9% | 39.7 / 12.0 | 29 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 5,740,467 | 0 | T | G | 25.0% | 50.0 / 21.9 | 44 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 4,340,081 | 0 | A | G | 24.1% | 46.9 / 11.5 | 29 | intergenic (+66/‑265) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,013,248 | 0 | A | T | 23.4% | 77.9 / 24.3 | 47 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 5,740,471 | 0 | A | T | 23.3% | 64.1 / 19.8 | 43 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 358,085 | 0 | A | G | 22.9% | 77.1 / 23.0 | 48 | intergenic (+53/‑77) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 358,096 | 0 | C | T | 22.9% | 85.5 / 22.8 | 51 | intergenic (+64/‑66) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 1,013,249 | 0 | T | G | 22.9% | 83.0 / 24.3 | 49 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947 | 358,087 | 0 | C | T | 22.4% | 85.7 / 21.9 | 50 | intergenic (+55/‑75) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 358,091 | 0 | G | A | 22.4% | 87.0 / 21.4 | 50 | intergenic (+59/‑71) | tdcG‑I/PP_5441 | L‑serine dehydratase/hypothetical protein |
| * | NC_002947 | 322,133 | 0 | G | A | 22.1% | 129.6 / 31.4 | 68 | intergenic (+420/+38) | aguA/PP_0267 | agmatine deiminase/ferric siderophore receptor |
| Marginal new junction evidence (lowest skew 10 of 327 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4808179 | 6 (0.090) | 29 (0.470) | 14/258 | 4.6 | 50.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 52 (0.840) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4852453 | 18 (0.270) | 9 (0.190) | 9/200 | 4.9 | 24.8% | intergenic (‑124/+173) | recR/ybaB | recombination protein RecR/nucleoid‑associated broad specificity regulator |
| ? | NC_002947 | = 4852512 | 42 (0.880) | intergenic (‑183/+114) | recR/ybaB | recombination protein RecR/nucleoid‑associated broad specificity regulator | |||||
| * | ? | NC_002947 | 4586034 = | 29 (0.430) | 12 (0.210) | 11/238 | 5.1 | 33.1% | intergenic (+117/+98) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586105 = | 24 (0.420) | intergenic (+188/+27) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 652782 | 60 (0.890) | 12 (0.210) | 11/242 | 5.2 | 31.8% | 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 | = 511918 | 86 (1.270) | 10 (0.170) | 10/252 | 5.8 | 12.9% | intergenic (+58/‑90) | trpC/PP_0423 | indole‑3‑glycerol phosphate synthase/hypothetical protein |
| ? | NC_002947 | = 511966 | 58 (0.960) | intergenic (+106/‑42) | trpC/PP_0423 | indole‑3‑glycerol phosphate synthase/hypothetical protein | |||||
| * | ? | NC_002947 | = 612221 | NA (NA) | 11 (0.220) +36 bp |
7/210 | 6.0 | 12.6% | intergenic (+152/+65) | PP_0526/dxs | transposase/1‑deoxyxylulose‑5‑phosphate synthase |
| ? | NC_002947 | = 2436665 | 103 (1.520) | intergenic (+243/‑416) | PP_2134/fadB | transposase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase | |||||
| * | ? | NC_002947 | 1114870 = | 58 (0.860) | 8 (0.140) | 8/232 | 6.1 | 15.0% | intergenic (‑64/+115) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase |
| ? | NC_002947 | 1114946 = | 43 (0.770) | intergenic (‑140/+39) | rlmF/valS | ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase | |||||
| * | ? | NC_002947 | 2957072 = | 69 (1.020) | 10 (0.170) | 9/252 | 6.2 | 13.5% | intergenic (+27/‑169) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947 | 2957159 = | 67 (1.110) | intergenic (+114/‑82) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947 | = 5201615 | 25 (0.370) | 6 (0.120) | 6/208 | 6.4 | 25.3% | intergenic (‑101/‑79) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | = 5201636 | 17 (0.340) | intergenic (‑122/‑58) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||
| * | ? | NC_002947 | 5382398 = | 34 (0.500) | 6 (0.120) | 6/212 | 6.5 | 18.3% | intergenic (+18/+115) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947 | 5382496 = | 28 (0.550) | intergenic (+116/+17) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||