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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_tpiA | 4,159,076 | 0 | T | A | 68.8% | 278.4 / 163.1 | 170 | L224Q (CTG→CAG) | oxyR | oxidative and nitrosative stress transcriptional regulator |
| * | NC_000913_3_pae_tpiA | 4,186,457 | 0 | A | G | 66.5% | 185.2 / 151.9 | 161 | K398E (AAG→GAG) | rpoC | RNA polymerase, beta prime subunit |
| * | NC_000913_3_pae_tpiA | 4,110,974 | 0 | C | A | 64.4% | 102.9 / 157.6 | 132 | intergenic (+289/+557) | cdh/yiiQ | CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein |
| * | NC_000913_3_pae_tpiA | 3,815,801 | 0 | A | . | 44.5% | 314.6 / 277.0 | 147 | intergenic (‑33/+33) | pyrE/rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| * | NC_000913_3_pae_tpiA | 3,440,923 | 0 | C | T | 36.5% | 153.1 / 177.6 | 167 | G36D (GGC→GAC) | rpoA | RNA polymerase, alpha subunit |
| * | NC_000913_3_pae_tpiA | 4,158,703 | 0 | A | G | 31.7% | 189.8 / 117.2 | 142 | T100A (ACA→GCA) | oxyR | oxidative and nitrosative stress transcriptional regulator |
| * | NC_000913_3_pae_tpiA | 4,295,976 | 0 | C | T | 24.5% | 451.9 / 151.5 | 245 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Marginal new junction evidence (lowest skew 10 of 1096 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | = 1755691 | 97 (0.560) | 108 (0.630) | 47/244 | 5.6 | 52.9% | intergenic (‑550/‑7) | ydhZ/pykF | uncharacterized protein/pyruvate kinase I |
| ? | NC_000913_3_pae_tpiA | = 2290112 | NA (NA) | intergenic (‑31/+2) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913_3_pae_tpiA | 1217413 = | 115 (0.660) | 53 (0.300) | 44/246 | 6.2 | 31.6% | coding (86/1524 nt) | ycgG | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| ? | NC_000913_3_pae_tpiA | = 1469240 | NA (NA) | intergenic (‑91/‑1) | insC1/ydbA | IS2 repressor TnpA/pseudogene, autotransporter homolog; interrupted by IS2 and IS30 | |||||
| * | ? | NC_000913_3_pae_tpiA | 1755687 = | 102 (0.590) | 85 (0.490) | 42/246 | 6.5 | 45.5% | intergenic (‑546/‑11) | ydhZ/pykF | uncharacterized protein/pyruvate kinase I |
| ? | NC_000913_3_pae_tpiA | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913_3_pae_tpiA | 1097172 = | NA (NA) | 46 (0.270) | 38/240 | 7.1 | 30.6% | intergenic (+343/+393) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_pae_tpiA | 1097188 = | 107 (0.610) | intergenic (+359/+377) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913_3_pae_tpiA | 1096988 = | 142 (0.820) | 45 (0.260) | 37/240 | 7.3 | 24.5% | intergenic (+159/+577) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_pae_tpiA | 1097191 = | NA (NA) | intergenic (+362/+374) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913_3_pae_tpiA | 59280 = | 160 (0.920) | 31 (0.210) | 27/212 | 8.5 | 18.8% | intergenic (+1/+407) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| ? | NC_000913_3_pae_tpiA | 59320 = | 130 (0.870) | intergenic (+41/+367) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent | |||||
| * | ? | NC_000913_3_pae_tpiA | 2464211 = | 207 (1.190) | 30 (0.190) | 28/220 | 8.6 | 13.8% | intergenic (+141/+41) | yfdF/mlaA | uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| ? | NC_000913_3_pae_tpiA | 2464243 = | 191 (1.230) | intergenic (+173/+9) | yfdF/mlaA | uncharacterized protein/ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1217417 | 105 (0.600) | 36 (0.210) | 32/246 | 8.6 | 25.5% | coding (90/1524 nt) | ycgG | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| ? | NC_000913_3_pae_tpiA | 1467910 = | NA (NA) | intergenic (+6/+11) | ydbA/insD1 | pseudogene, autotransporter homolog; interrupted by IS2 and IS30/IS2 transposase TnpB | |||||
| * | ? | NC_000913_3_pae_tpiA | = 3423389 | 206 (1.180) | 31 (0.200) | 27/218 | 8.7 | 14.5% | intergenic (+195/+34) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| ? | NC_000913_3_pae_tpiA | = 3423405 | 182 (1.180) | intergenic (+211/+18) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon | |||||
| * | ? | NC_000913_3_pae_tpiA | 1097007 = | 140 (0.800) | 33 (0.190) | 30/240 | 8.9 | 19.5% | intergenic (+178/+558) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_pae_tpiA | 1097172 = | NA (NA) | intergenic (+343/+393) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||