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 32 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 297,897 | 0 | C | T | 52.4% | 491.0 / inf | 1204 | E130K (GAG→AAG) | paoA | PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit |
| * | CP009273 | 309,254 | 0 | G | A | 52.3% | 392.1 / inf | 977 | intergenic (‑301/+173) | ykgR/ykgP | uncharacterized protein/pseudogene, oxidoreductase family |
| * | CP009273 | 580,748 | 0 | G | T | 27.6% | 1166.4 / inf | 656 | T114T (ACC→ACA) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,784 | 0 | G | A | 27.1% | 1146.3 / inf | 632 | V102V (GTC→GTT) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,802 | 0 | G | A | 26.8% | 1192.1 / inf | 637 | S96S (AGC→AGT) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,805 | 0 | G | A | 26.8% | 1205.7 / inf | 639 | G95G (GGC→GGT) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,793 | 0 | G | C | 26.6% | 1379.3 / inf | 644 | G99G (GGC→GGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,807 | 0 | C | T | 26.6% | 1226.0 / inf | 634 | G95S (GGC→AGC) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,806 | 0 | C | T | 26.6% | 1239.2 / inf | 635 | G95D (GGC→GAC) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,814 | 0 | T | G | 26.5% | 1319.9 / inf | 648 | T92T (ACA→ACC) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,796 | 0 | A | C | 26.4% | 1256.3 / inf | 644 | G98G (GGT→GGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,758 | 0 | T | G | 26.2% | 1245.6 / inf | 621 | N111T (AAC→ACC) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,799 | 0 | T | C | 26.2% | 1502.6 / inf | 646 | R97R (CGA→CGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,757 | 0 | G | A | 26.2% | 1160.6 / inf | 611 | N111N (AAC→AAT) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,762 | 0 | T | C | 26.1% | 1452.7 / inf | 617 | S110G (AGT→GGT) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,760 | 0 | A | C | 26.1% | 1247.2 / inf | 620 | S110R (AGT→AGG) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 3,774,404 | 0 | T | A | 25.8% | 402.7 / 42.0 | 189 | intergenic (+27/‑171) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| * | CP009273 | 580,742 | 0 | C | T | 25.7% | 1241.3 / inf | 626 | T116T (ACG→ACA) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 161,051 | 0 | A | T | 24.2% | 217.4 / 21.1 | 128 | intergenic (+30/‑166) | hrpB/mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| * | CP009273 | 3,774,398 | 0 | T | A | 23.4% | 434.2 / 25.8 | 197 | intergenic (+21/‑177) | lldD/trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| Marginal new junction evidence (lowest skew 10 of 107 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 776778 | 171 (0.510) | 30 (0.120) | 24/220 | 15.1 | 20.2% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | CP009273 | 777267 = | 111 (0.450) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | = 4285798 | 239 (0.720) | 20 (0.080) | 16/220 | 18.6 | 8.6% | noncoding (76/530 nt) | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 4286251 = | 250 (1.020) | noncoding (529/530 nt) | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | CP009273 | = 776778 | 171 (0.510) | 14 (0.060) | 13/220 | 20.1 | 9.1% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | CP009273 | 2514846 = | 154 (0.630) | noncoding (574/1345 nt) | IS186 | repeat region | |||||
| * | ? | CP009273 | = 776472 | 149 (0.450) | 12 (0.050) | 11/224 | 21.5 | 9.6% | intergenic (+98/‑52) | lysW/valZ | tRNA‑Lys/tRNA‑Val |
| ? | CP009273 | 777265 = | 115 (0.460) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | 921313 = | 225 (0.680) | 17 (0.070) | 8/206 | 22.3 | 12.1% | intergenic (+317/+27) | clpA/serW | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser |
| ? | CP009273 | = 1092631 | 91 (0.400) | intergenic (+346/+390) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | CP009273 | = 776678 | 176 (0.530) | 17 (0.060) | 13/262 | 22.6 | 10.1% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | CP009273 | 777265 = | 148 (0.510) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | = 2811301 | 190 (0.570) | 17 (0.060) | 12/258 | 22.9 | 8.0% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | CP009273 | 2811851 = | 228 (0.790) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | CP009273 | = 1282540 | 204 (0.610) | 14 (0.050) | 11/258 | 23.5 | 7.1% | noncoding (153/171 nt) | rttR | rtT sRNA, processed from tyrT transcript |
| ? | CP009273 | 1283013 = | 188 (0.650) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | CP009273 | = 2897461 | 376 (1.130) | 9 (0.030) | 9/238 | 23.6 | 2.7% | intergenic (+728/+645) | ygcE/queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| ? | CP009273 | 2897767 = | 352 (1.330) | intergenic (+1034/+339) | ygcE/queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis | |||||
| * | ? | CP009273 | = 2871151 | 428 (1.290) | 11 (0.040) | 11/260 | 23.6 | 3.0% | intergenic (+174/+777) | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease |
| ? | CP009273 | 2871642 = | 337 (1.160) | intergenic (+665/+286) | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/CRISPR adaptation ssRNA endonuclease | |||||