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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 60.0% | ‑4.5 / 42.0 | 40 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,348,705 | 0 | A | G | 52.3% | 1.9 / 116.0 | 88 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,722 | 0 | A | G | 50.0% | ‑0.9 / 30.6 | 24 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 35.8% | 107.2 / 100.7 | 111 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,351 | 0 | C | G | 33.3% | 147.6 / 102.1 | 103 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,905 | 0 | T | C | 28.0% | 70.3 / 33.3 | 50 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,911 | 0 | A | . | 27.8% | 128.4 / 55.4 | 54 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 196,327 | 0 | A | C | 27.4% | 209.9 / 92.9 | 117 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,390 | 0 | T | C | 26.9% | 120.5 / 51.7 | 79 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 195,559 | 0 | C | A | 23.1% | 151.6 / 35.7 | 66 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,306 | 0 | T | C | 22.1% | 251.9 / 63.8 | 122 | N604N (AAT→AAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 197,695 | 0 | G | C | 21.5% | 162.2 / 30.1 | 65 | T1067T (ACG→ACC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,894 | 0 | C | T | 20.4% | 90.6 / 17.5 | 44 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,895 | 0 | A | G | 20.4% | 81.0 / 17.7 | 44 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 1780066 | 24 (0.420) | 7 (0.130) | 7/268 | 4.2 | 24.2% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | 1780129 = | 21 (0.390) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | = 652782 | 47 (0.820) | 6 (0.120) | 6/242 | 4.2 | 22.9% | 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 | = 5622412 | 82 (1.430) | 4 (0.080) | 4/260 | 5.2 | 5.2% | coding (1326/1404 nt) | PP_4941 | hypothetical protein |
| ? | NC_002947 | = 5622499 | 69 (1.310) | coding (1239/1404 nt) | PP_4941 | hypothetical protein | |||||
| * | ? | NC_002947 | = 5605866 | 58 (1.010) | 4 (0.070) | 4/266 | 5.3 | 7.7% | coding (81/1419 nt) | PP_4926 | HlyD family secretion protein |
| ? | NC_002947 | = 5605950 | 41 (0.760) | coding (2189/2196 nt) | cyaB | cyclolysin secretion/processing ATP‑binding protein CyaB | |||||
| * | ? | NC_002947 | = 4808179 | 0 (0.000) | 9 (0.170) | 3/258 | 5.6 | 35.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988765 = | 33 (0.630) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 5264837 = | 67 (1.170) | 3 (0.060) | 3/268 | 5.7 | 4.9% | coding (1775/2067 nt) | yjiY | putative transporter |
| ? | NC_002947 | 5264917 = | 53 (0.970) | coding (1695/2067 nt) | yjiY | putative transporter | |||||
| * | ? | NC_002947 | 4601529 = | 55 (0.960) | 3 (0.060) | 3/266 | 5.7 | 5.4% | coding (363/633 nt) | PP_4073 | hypothetical protein |
| ? | NC_002947 | 4601591 = | 54 (1.000) | coding (301/633 nt) | PP_4073 | hypothetical protein | |||||
| * | ? | NC_002947 | = 3708260 | 38 (0.660) | 3 (0.060) | 3/266 | 5.7 | 7.0% | coding (614/1563 nt) | actP‑III | acetate permease |
| ? | NC_002947 | = 3708293 | 44 (0.810) | coding (581/1563 nt) | actP‑III | acetate permease | |||||
| * | ? | NC_002947 | 3494883 = | 68 (1.190) | 3 (0.060) | 3/266 | 5.7 | 4.4% | coding (1331/1503 nt) | puuD | uricase/urate oxidase |
| ? | NC_002947 | 3494924 = | 65 (1.200) | coding (1290/1503 nt) | puuD | uricase/urate oxidase | |||||
| * | ? | NC_002947 | 5093419 = | 81 (1.410) | 5 (0.090) | 3/274 | 5.8 | 6.0% | coding (203/981 nt) | PP_4482 | AraC family transcriptional regulator |
| ? | NC_002947 | 5093466 = | 77 (1.380) | coding (156/981 nt) | PP_4482 | AraC family transcriptional regulator | |||||