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 | ||
| * | CP009273 | 309,254 | 0 | G | A | 64.3% | 989.7 / inf | 652 | intergenic (‑301/+173) | ykgR/ykgP | uncharacterized protein/pseudogene, oxidoreductase family |
| * | CP009273 | 297,897 | 0 | C | T | 62.5% | 1156.3 / inf | 883 | E130K (GAG→AAG) | paoA | PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit |
| * | CP009273 | 161,068 | 0 | A | C | 27.2% | 204.8 / 29.2 | 149 | intergenic (+47/‑149) | hrpB/mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| * | CP009273 | 2,222,683 | 0 | T | A | 25.2% | 303.1 / 42.0 | 164 | intergenic (+139/+234) | yohP/dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| * | CP009273 | 1,264,647 | 0 | T | C | 24.6% | 255.4 / 74.8 | 117 | S29G (AGC→GGC) | ldrA | toxic polypeptide, small |
| * | CP009273 | 2,222,669 | 0 | T | A | 22.8% | 317.1 / 42.7 | 164 | intergenic (+125/+248) | yohP/dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| * | CP009273 | 580,748 | 0 | G | T | 22.3% | 853.7 / 259.9 | 372 | T114T (ACC→ACA) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,793 | 0 | G | C | 22.0% | 888.5 / 278.4 | 346 | G99G (GGC→GGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,799 | 0 | T | C | 21.9% | 940.1 / 249.5 | 347 | R97R (CGA→CGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,796 | 0 | A | C | 21.8% | 823.5 / 240.7 | 349 | G98G (GGT→GGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,802 | 0 | G | A | 21.8% | 823.5 / 272.6 | 349 | S96S (AGC→AGT) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,805 | 0 | G | A | 21.8% | 821.8 / 266.5 | 351 | G95G (GGC→GGT) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,784 | 0 | G | A | 21.6% | 818.6 / 274.5 | 351 | V102V (GTC→GTT) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,814 | 0 | T | G | 21.5% | 873.8 / 238.2 | 358 | T92T (ACA→ACC) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 3,774,404 | 0 | T | A | 21.1% | 567.7 / 36.1 | 219 | intergenic (+27/‑171) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | CP009273 | 580,807 | 0 | C | T | 21.1% | 849.6 / 262.9 | 357 | G95S (GGC→AGC) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,806 | 0 | C | T | 20.8% | 851.4 / 263.1 | 357 | G95D (GGC→GAC) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,742 | 0 | C | T | 20.7% | 846.0 / 261.3 | 355 | T116T (ACG→ACA) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| Marginal new junction evidence (lowest skew 10 of 89 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 776778 | 176 (0.540) | 18 (0.070) | 17/222 | 16.7 | 11.5% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | CP009273 | 777267 = | 147 (0.610) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | = 776472 | 182 (0.560) | 15 (0.060) | 15/226 | 17.9 | 9.6% | intergenic (+98/‑52) | lysW/valZ | tRNA‑Lys/tRNA‑Val |
| ? | CP009273 | 777265 = | 147 (0.600) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | = 776678 | 173 (0.530) | 29 (0.100) | 17/264 | 18.9 | 14.8% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | CP009273 | 777265 = | 183 (0.640) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | = 4120094 | 397 (1.210) | 19 (0.060) | 17/276 | 19.4 | 5.1% | coding (332/2433 nt) | metL | Bifunctional aspartokinase/homoserine dehydrogenase 2 |
| ? | CP009273 | 4120557 = | 345 (1.140) | coding (795/2433 nt) | metL | Bifunctional aspartokinase/homoserine dehydrogenase 2 | |||||
| * | ? | CP009273 | = 4285798 | 251 (0.770) | 12 (0.050) | 11/222 | 19.7 | 5.2% | noncoding (76/530 nt) | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 4286251 = | 251 (1.040) | noncoding (529/530 nt) | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | CP009273 | = 776738 | 165 (0.500) | 17 (0.050) | 16/284 | 20.2 | 9.3% | intergenic (+60/‑87) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | CP009273 | 777227 = | 176 (0.570) | intergenic (+119/‑314) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | 776825 = | 194 (0.590) | 21 (0.060) +G |
16/298 | 20.8 | 8.7% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
| ? | CP009273 | = 2514486 | 251 (0.770) | noncoding (214/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | = 2811027 | 281 (0.860) | 17 (0.060) | 12/258 | 21.0 | 7.9% | intergenic (‑165/+116) | yqaB/argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| ? | CP009273 | 2811575 = | 154 (0.550) | noncoding (59/77 nt) | argY | tRNA‑Arg | |||||
| * | ? | CP009273 | = 1282540 | 209 (0.640) | 15 (0.050) | 12/260 | 21.1 | 7.5% | noncoding (153/171 nt) | rttR | rtT sRNA, processed from tyrT transcript |
| ? | CP009273 | 1283013 = | 188 (0.660) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | CP009273 | 921313 = | 278 (0.850) | 39 (0.170) | 7/208 | 21.4 | 18.6% | intergenic (+317/+27) | clpA/serW | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser |
| ? | CP009273 | = 1092450 | 149 (0.660) | intergenic (+165/+571) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||