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 24 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 309,254 | 0 | G | A | 61.1% | 827.3 / inf | 690 | intergenic (‑301/+173) | ykgR/ykgP | uncharacterized protein/pseudogene, oxidoreductase family |
| * | CP009273 | 297,897 | 0 | C | T | 58.3% | 810.4 / inf | 838 | E130K (GAG→AAG) | paoA | PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit |
| * | CP009273 | 3,045,676 | 0 | T | C | 36.7% | 78.0 / 69.7 | 60 | M1M (ATG→GTG) † | ubiI | 2‑octaprenylphenol hydroxylase, FAD‑dependent |
| * | CP009273 | 3,045,666 | 0 | A | G | 29.8% | 108.6 / 51.2 | 57 | V4A (GTT→GCT) | ubiI | 2‑octaprenylphenol hydroxylase, FAD‑dependent |
| * | CP009273 | 2,222,669 | 0 | T | A | 25.8% | 367.8 / 49.2 | 184 | intergenic (+125/+248) | yohP/dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| * | CP009273 | 161,068 | 0 | A | C | 25.7% | 218.4 / 20.3 | 144 | intergenic (+47/‑149) | hrpB/mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| * | CP009273 | 3,774,404 | 0 | T | A | 24.3% | 517.1 / 43.4 | 214 | intergenic (+27/‑171) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | CP009273 | 580,748 | 0 | G | T | 22.6% | 865.7 / 269.9 | 376 | T114T (ACC→ACA) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 2,222,683 | 0 | T | A | 22.2% | 394.8 / 48.7 | 188 | intergenic (+139/+234) | yohP/dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| * | CP009273 | 2,222,692 | 0 | G | C | 21.8% | 406.7 / 69.7 | 179 | intergenic (+148/+225) | yohP/dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| * | CP009273 | 580,742 | 0 | C | T | 21.7% | 846.4 / 285.2 | 370 | T116T (ACG→ACA) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,793 | 0 | G | C | 21.3% | 948.3 / 264.9 | 357 | G99G (GGC→GGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,784 | 0 | G | A | 21.2% | 821.6 / 268.2 | 355 | V102V (GTC→GTT) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,757 | 0 | G | A | 21.1% | 859.1 / 275.6 | 365 | N111N (AAC→AAT) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,760 | 0 | A | C | 21.1% | 911.8 / 245.8 | 369 | S110R (AGT→AGG) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,796 | 0 | A | C | 21.1% | 884.7 / 236.6 | 361 | G98G (GGT→GGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,762 | 0 | T | C | 21.0% | 1030.9 / 243.7 | 369 | S110G (AGT→GGT) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,799 | 0 | T | C | 20.9% | 1009.6 / 241.7 | 363 | R97R (CGA→CGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,758 | 0 | T | G | 20.9% | 907.3 / 240.2 | 369 | N111T (AAC→ACC) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,802 | 0 | G | A | 20.7% | 861.3 / 262.5 | 363 | S96S (AGC→AGT) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| Marginal new junction evidence (lowest skew 10 of 102 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 776778 | 199 (0.590) | 26 (0.100) | 24/222 | 17.9 | 15.3% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | CP009273 | 777267 = | 140 (0.560) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | = 776472 | 168 (0.500) | 18 (0.070) | 16/226 | 22.1 | 11.7% | intergenic (+98/‑52) | lysW/valZ | tRNA‑Lys/tRNA‑Val |
| ? | CP009273 | 777265 = | 145 (0.570) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | = 1282362 | 239 (0.710) | 20 (0.070) | 20/260 | 22.4 | 9.2% | intergenic (+380/+160) | narI/rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| ? | CP009273 | 1283013 = | 186 (0.640) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | CP009273 | = 2811301 | 263 (0.780) | 21 (0.070) | 15/260 | 25.1 | 8.7% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | CP009273 | 2811851 = | 214 (0.730) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | CP009273 | = 243984 | NA (NA) | 16 (0.060) +24 bp |
14/252 | 25.1 | NA | noncoding (40/84 nt) | REP18 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP18 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | CP009273 | 244650 = | NA (NA) | noncoding (17/188 nt) | REP19 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP19 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | = 2871151 | 426 (1.260) | 15 (0.050) | 15/262 | 25.2 | 3.7% | intergenic (+174/+777) | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease |
| ? | CP009273 | 2871825 = | 406 (1.380) | intergenic (+848/+103) | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease | |||||
| * | ? | CP009273 | = 2871150 | 438 (1.300) | 16 (0.050) | 14/264 | 25.9 | 4.1% | intergenic (+173/+778) | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease |
| ? | CP009273 | 2871763 = | 361 (1.220) | intergenic (+786/+165) | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease | |||||
| * | ? | CP009273 | = 776738 | 202 (0.600) | 16 (0.050) | 16/284 | 26.0 | 7.7% | intergenic (+60/‑87) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | CP009273 | 777227 = | 190 (0.590) | intergenic (+119/‑314) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | = 4285798 | 287 (0.850) | 11 (0.040) | 9/222 | 26.3 | 4.3% | noncoding (76/530 nt) | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 4286251 = | 281 (1.130) | noncoding (529/530 nt) | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | CP009273 | = 2871271 | 494 (1.460) | 11 (0.040) | 11/242 | 26.3 | 2.7% | intergenic (+294/+657) | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease |
| ? | CP009273 | 2871823 = | 386 (1.420) | intergenic (+846/+105) | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease | |||||