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 34 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 | 58.5% | 4.7 / 54.7 | 41 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | JE3692‑4 | 1,327,121 | 0 | C | T | 55.2% | 34.9 / 208.6 | 134 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | JE3692‑4 | 4,360,849 | 0 | A | G | 54.4% | ‑4.8 / 250.6 | 160 | intergenic (‑70/+404) | PP_3820/PP_3821 | Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | JE3692‑4 | 196,390 | 0 | T | C | 41.3% | 213.3 / 259.2 | 189 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 195,634 | 0 | C | T | 39.3% | 221.3 / 212.2 | 163 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 196,351 | 0 | C | G | 39.0% | 294.9 / inf | 246 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 4,820,324 | 0 | A | C | 38.5% | 6.9 / 13.8 | 14 | 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 | 38.5% | 8.0 / 12.1 | 14 | 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 | 30.5% | 96.3 / 30.8 | 66 | G226G (GGC→GGG) | PP_3195 | conserved protein of unknown function |
| * | JE3692‑4 | 5,301,739 | 0 | G | C | 29.5% | 100.0 / 22.0 | 44 | A244G (GCC→GGC) | PP_4663 | conserved transmembrane protein of unknown function |
| * | JE3692‑4 | 196,327 | 0 | A | C | 28.2% | 410.1 / 235.0 | 234 | T611T (ACA→ACC) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 1,296,458 | 0 | A | C | 27.0% | 218.2 / 12.0 | 89 | intergenic (‑211/‑355) | PP_1132/PP_1133 | Na(+)/H(+) antiporter NhaA 1/transposase |
| * | JE3692‑4 | 316,226 | 0 | G | C | 25.8% | 172.5 / 28.8 | 71 | A100G (GCG→GGG) | PP_0262 | conserved protein of unknown function |
| * | JE3692‑4 | 324,670 | 0 | C | T | 25.0% | 184.9 / 37.6 | 94 | intergenic (‑430/‑45) | PP_0267/PP_0268 | putative Outer membrane ferric siderophore receptor/outer‑membrane porin D |
| * | JE3692‑4 | 197,590 | 0 | T | C | 24.7% | 396.2 / 142.5 | 187 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 4,069,521 | 0 | G | C | 23.9% | 184.5 / 28.5 | 76 | G95G (GGC→GGG) | PP_3575 | Outer membrane ferric siderophore receptor |
| * | JE3692‑4 | 4,385,661 | 0 | C | T | 23.7% | 251.0 / 41.7 | 115 | G177G (GGC→GGT) | PP_3849 | putative calcium‑binding protein, hemolysin‑type |
| * | JE3692‑4 | 4,479,807 | 0 | G | C | 23.5% | 235.9 / 34.0 | 85 | intergenic (+44/‑93) | PP_3958/PP_3959 | Na(+)/H(+) antiporter NhaA 2/Voltage‑gated chloride channel family protein |
| * | JE3692‑4 | 3,324,826 | 0 | G | T | 22.9% | 166.1 / 10.3 | 61 | intergenic (+23/‑139) | PP_2912/PP_2913 | conserved protein of unknown function/5‑aminolevulinate dehydratase |
| * | JE3692‑4 | 4,341,110 | 0 | G | C | 22.2% | 150.5 / 18.1 | 55 | D72H (GAC→CAC) | PP_3799 | conserved exported protein of unknown function |
| Marginal new junction evidence (lowest skew 10 of 122 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | = 4992729 | 1 (0.010) | 58 (0.510) +GGC |
38/186 | 3.4 | 98.4% | intergenic (‑24/+44) | PP_4387/PP_4388 | conserved exported protein of unknown function/Flagellar hook protein FlgE |
| ? | JE3692‑4 | 4992730 = | 1 (0.010) | intergenic (‑25/+43) | PP_4387/PP_4388 | conserved exported protein of unknown function/Flagellar hook protein FlgE | |||||
| * | ? | JE3692‑4 | = 652782 | 58 (0.490) | 30 (0.320) | 24/152 | 4.6 | 56.2% | 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 | = 4820323 | 7 (0.060) | 24 (0.260) | 21/152 | 5.4 | 56.1% | intergenic (‑288/‑267) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | = 6000025 | 32 (0.340) | intergenic (+243/‑303) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 4820323 | 7 (0.060) | 23 (0.220) | 20/168 | 6.5 | 40.3% | intergenic (‑288/‑267) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | 5999841 = | 62 (0.600) | intergenic (+59/‑487) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 652782 | 58 (0.490) | 6 (0.070) +29 bp |
6/134 | 10.5 | 18.1% | coding (1961/1962 nt) | PP_0562 | Methyl‑accepting chemotaxis protein CtpL |
| ? | JE3692‑4 | = 4820306 | 20 (0.170) | intergenic (‑271/‑284) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | 611741 = | NA (NA) | 11 (0.100) | 11/186 | 10.7 | NA | noncoding (842/1314 nt) | mobile_element | repeat region |
| ? | JE3692‑4 | 611766 = | NA (NA) | noncoding (867/1314 nt) | mobile_element | repeat region | |||||
| * | ? | JE3692‑4 | = 4820274 | 41 (0.350) | 15 (0.130) | 10/186 | 11.1 | 26.9% | intergenic (‑239/‑316) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | = 6000042 | 42 (0.370) | intergenic (+260/‑286) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | 4820317 = | 16 (0.140) | 12 (0.100) | 9/188 | 11.7 | 20.4% | intergenic (‑282/‑273) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | = 4957516 | 78 (0.670) | intergenic (+732/+66) | PP_5673/PP_4352 | putative D‑alanine‑‑D‑alanine ligase/flagellin export apparatus, substrate specificity protein | |||||
| * | ? | JE3692‑4 | = 4820306 | 20 (0.170) | 3 (0.040) +29 bp |
3/134 | 12.7 | 10.8% | intergenic (‑271/‑284) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | = 6000045 | 51 (0.430) | intergenic (+263/‑283) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 5999847 | 70 (0.590) | 7 (0.060) | 6/176 | 12.8 | 11.5% | intergenic (+65/‑481) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | JE3692‑4 | 6000039 = | 44 (0.410) | intergenic (+257/‑289) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||