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 48 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | JE3692‑4 | 4,976,769 | 0 | C | A | 62.2% | 91.6 / 144.4 | 111 | D245Y (GAC→TAC) | PP_4373 | Transcriptional regulator FleQ |
| * | JE3692‑4 | 1,703,539 | 0 | C | T | 57.8% | 65.4 / 160.3 | 116 | S647L (TCG→TTG) | PP_1492 | Sensor histidine kinase/response regulator |
| * | JE3692‑4 | 1,327,121 | 0 | C | T | 51.9% | 56.0 / 209.0 | 134 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | JE3692‑4 | 4,360,849 | 0 | A | G | 50.9% | 34.0 / 264.0 | 162 | intergenic (‑70/+404) | PP_3820/PP_3821 | Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | JE3692‑4 | 699,722 | 0 | A | G | 45.5% | 45.3 / 146.2 | 99 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | JE3692‑4 | 4,820,324 | 0 | A | C | 45.5% | 3.1 / 13.5 | 11 | 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 | 45.5% | 3.0 / 11.8 | 11 | intergenic (‑290/‑265) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | JE3692‑4 | 3,636,954 | 0 | G | C | 35.6% | 47.2 / 28.5 | 48 | G226G (GGC→GGG) | PP_3195 | conserved protein of unknown function |
| * | JE3692‑4 | 5,563,987 | 0 | G | T | 34.5% | 101.4 / 21.5 | 55 | intergenic (+574/+87) | PP_4882/PP_5717 | Iron ABC transporter, permease protein/conserved protein of unknown function |
| * | JE3692‑4 | 1,927,172 | 0 | T | C | 33.3% | 85.7 / 25.6 | 54 | intergenic (+15/+46) | PP_1720/PP_1721 | Alcohol dehydrogenase, zinc‑containing/putative phosphoserine phosphatase |
| * | JE3692‑4 | 195,634 | 0 | C | T | 31.5% | 360.8 / 199.3 | 200 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 5,999,965 | 0 | C | A | 30.2% | 196.3 / 78.2 | 86 | intergenic (+183/‑363) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,999,970 | 0 | C | T | 30.0% | 185.3 / 77.0 | 90 | intergenic (+188/‑358) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,999,971 | 0 | A | G | 30.0% | 187.2 / 78.2 | 90 | intergenic (+189/‑357) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,192,788 | 0 | T | G | 29.8% | 117.4 / 11.0 | 67 | K115Q (AAG→CAG) | PP_4559 | peptide deformylase |
| * | JE3692‑4 | 196,390 | 0 | T | C | 29.0% | 267.0 / 125.3 | 148 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 1,938,270 | 0 | G | C | 28.6% | 41.9 / 21.6 | 28 | intergenic (‑105/+45) | PP_1731/PP_1732 | 23S rRNA (746) and tRNA (32) pseudouridine synthase/Cell division topological specificity factor |
| * | JE3692‑4 | 5,999,981 | 0 | T | C | 28.4% | 210.8 / 73.7 | 95 | intergenic (+199/‑347) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 5,999,987 | 0 | A | . | 28.4% | 252.1 / 105.5 | 88 | intergenic (+205/‑341) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | JE3692‑4 | 196,351 | 0 | C | G | 28.3% | 338.2 / 180.0 | 188 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 874 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | = 652783 | 119 (1.180) | 20 (0.310) | 13/126 | 5.3 | 34.3% | 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 = | 19 (0.190) | 20 (0.270) | 13/144 | 6.3 | 39.2% | intergenic (‑283/‑272) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | 5999855 = | 48 (0.650) | intergenic (+73/‑473) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 652782 | 119 (1.180) | 11 (0.150) +29 bp |
9/138 | 7.7 | 18.1% | coding (1961/1962 nt) | PP_0562 | Methyl‑accepting chemotaxis protein CtpL |
| ? | JE3692‑4 | = 4820306 | 22 (0.220) | intergenic (‑271/‑284) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | = 173119 | NA (NA) | 16 (0.170) | 13/184 | 8.2 | NA | intergenic (+209/‑84) | PP_16SA/PP_23SA | 16S ribosomal RNA/23S ribosomal RNA |
| ? | JE3692‑4 | = 173149 | NA (NA) | intergenic (+239/‑54) | PP_16SA/PP_23SA | 16S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 2556265 | NA (NA) | 15 (0.160) | 12/184 | 8.6 | NA | intergenic (+160/‑84) | PP_t36/PP_23SF | tRNA‑Ala/23S ribosomal RNA |
| ? | JE3692‑4 | = 2556295 | NA (NA) | intergenic (+190/‑54) | PP_t36/PP_23SF | tRNA‑Ala/23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 5999835 | 68 (0.670) | 12 (0.130) | 11/182 | 9.0 | 15.2% | intergenic (+53/‑493) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | JE3692‑4 | 6000027 = | 71 (0.760) | intergenic (+245/‑301) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | 526263 = | NA (NA) | 13 (0.130) | 12/192 | 9.0 | NA | noncoding (1315/1522 nt) | PP_16SC | 16S ribosomal RNA |
| ? | JE3692‑4 | 526291 = | NA (NA) | noncoding (1343/1522 nt) | PP_16SC | 16S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 174673 = | NA (NA) | 16 (0.170) | 11/182 | 9.0 | NA | noncoding (1471/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | 174701 = | NA (NA) | noncoding (1499/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 173166 | NA (NA) | 13 (0.130) | 12/194 | 9.1 | NA | intergenic (+256/‑37) | 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 | 171518 = | NA (NA) | 13 (0.130) | 12/194 | 9.1 | NA | noncoding (130/1522 nt) | PP_16SA | 16S ribosomal RNA |
| ? | JE3692‑4 | 171538 = | NA (NA) | noncoding (150/1522 nt) | PP_16SA | 16S ribosomal RNA | |||||