mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 55 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | JE3692‑4 | 699,722 | 0 | A | G | 60.4% | 28.5 / 117.8 | 91 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | JE3692‑4 | 4,820,324 | 0 | A | C | 55.2% | ‑1.0 / 39.7 | 29 | intergenic (‑289/‑266) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | JE3692‑4 | 4,820,325 | 0 | A | G | 55.2% | ‑0.8 / 39.7 | 29 | intergenic (‑290/‑265) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | JE3692‑4 | 1,327,121 | 0 | C | T | 55.0% | 33.5 / 207.1 | 140 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | JE3692‑4 | 4,820,330 | 0 | C | T | 48.0% | 9.2 / 36.6 | 25 | intergenic (‑295/‑260) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | JE3692‑4 | 4,820,331 | 0 | G | T | 48.0% | 16.4 / 39.0 | 25 | intergenic (‑296/‑259) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | JE3692‑4 | 2,184,203 | 0 | T | C | 45.8% | 66.3 / 118.3 | 120 | N269N (AAT→AAC) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 4,365,337 | 0 | A | C | 45.1% | 59.2 / 12.4 | 51 | T107P (ACG→CCG) | PP_3827 | 2‑nitropropane dioxygenase |
| * | JE3692‑4 | 4,360,849 | 0 | A | G | 43.1% | 111.9 / 211.1 | 146 | intergenic (‑70/+404) | PP_3820/PP_3821 | Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | JE3692‑4 | 2,184,200 | 0 | G | A | 41.9% | 129.6 / 70.6 | 122 | T268T (ACG→ACA) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 195,634 | 0 | C | T | 40.3% | 196.9 / 203.0 | 155 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 1,592,599 | 0 | C | G | 36.1% | 49.9 / 22.0 | 40 | A65G (GCC→GGC) | PP_1397 | conserved protein of unknown function |
| * | JE3692‑4 | 2,184,204 | 0 | G | C | 34.6% | 177.4 / 68.5 | 119 | V270L (GTC→CTC) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 3,636,954 | 0 | G | C | 31.7% | 72.7 / 34.4 | 62 | G226G (GGC→GGG) | PP_3195 | conserved protein of unknown function |
| * | JE3692‑4 | 5,999,987 | 0 | A | . | 31.4% | 267.2 / 138.1 | 102 | intergenic (+205/‑341) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,999,981 | 0 | T | C | 30.5% | 214.9 / 82.4 | 105 | intergenic (+199/‑347) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 4,479,807 | 0 | G | C | 29.6% | 217.6 / 54.6 | 101 | intergenic (+44/‑93) | PP_3958/PP_3959 | Na(+)/H(+) antiporter NhaA 2/Voltage‑gated chloride channel family protein |
| * | JE3692‑4 | 196,351 | 0 | C | G | 29.0% | 422.5 / 249.3 | 246 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 324,670 | 0 | C | T | 28.7% | 188.9 / 66.4 | 122 | intergenic (‑430/‑45) | PP_0267/PP_0268 | putative Outer membrane ferric siderophore receptor/outer‑membrane porin D |
| * | JE3692‑4 | 5,999,971 | 0 | A | G | 27.8% | 256.9 / 93.9 | 116 | intergenic (+189/‑357) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 762 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | = 652782 | 99 (0.850) | 42 (0.450) | 28/156 | 3.6 | 51.3% | coding (1961/1962 nt) | PP_0562 | Methyl‑accepting chemotaxis protein CtpL |
| ? | JE3692‑4 | = 4820303 | 1 (0.010) | intergenic (‑268/‑287) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | = 652783 | 100 (0.860) | 23 (0.310) | 17/126 | 4.8 | 41.7% | coding (1960/1962 nt) | PP_0562 | Methyl‑accepting chemotaxis protein CtpL |
| ? | JE3692‑4 | 4820353 = | 0 (0.000) | intergenic (‑318/‑237) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | 4820318 = | 31 (0.270) | 25 (0.290) | 19/144 | 5.2 | 41.1% | intergenic (‑283/‑272) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | 5999855 = | 49 (0.570) | intergenic (+73/‑473) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 4820323 | 13 (0.110) | 30 (0.290) | 20/172 | 6.3 | 45.7% | intergenic (‑288/‑267) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | 5999841 = | 60 (0.590) | intergenic (+59/‑487) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 5999847 | 74 (0.640) | 17 (0.160) | 14/180 | 8.8 | 17.4% | intergenic (+65/‑481) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | JE3692‑4 | 6000039 = | 93 (0.870) | intergenic (+257/‑289) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 2477747 | 90 (0.770) | 15 (0.140) | 12/182 | 9.8 | 16.0% | intergenic (+19/+130) | PP_2166/PP_2167 | Anti‑anti‑sigma factor/putative PhoD‑like phosphatase |
| ? | JE3692‑4 | 2477945 = | 74 (0.680) | coding (1783/1851 nt) | PP_2167 | putative PhoD‑like phosphatase | |||||
| * | ? | JE3692‑4 | = 1785698 | 23 (0.200) | 11 (0.100) | 11/182 | 10.2 | 27.4% | intergenic (+25/+81) | PP_1587/PP_1588 | NhaP‑type Na+/H+ and K+/H+ antiporters/N‑succinyl‑L,L‑diaminopimelate aminotransferase alternative |
| ? | JE3692‑4 | 1785761 = | 37 (0.340) | intergenic (+88/+18) | PP_1587/PP_1588 | NhaP‑type Na+/H+ and K+/H+ antiporters/N‑succinyl‑L,L‑diaminopimelate aminotransferase alternative | |||||
| * | ? | JE3692‑4 | 173168 = | NA (NA) | 15 (0.140) | 11/182 | 10.2 | NA | intergenic (+258/‑35) | PP_16SA/PP_23SA | 16S ribosomal RNA/23S ribosomal RNA |
| ? | JE3692‑4 | 173216 = | NA (NA) | noncoding (14/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 175943 = | NA (NA) | 13 (0.120) | 11/186 | 10.4 | NA | noncoding (2741/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | 175972 = | NA (NA) | noncoding (2770/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 174571 = | NA (NA) | 13 (0.120) | 11/186 | 10.4 | NA | noncoding (1369/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | 174602 = | NA (NA) | noncoding (1400/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||