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 64 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 243,234 | 0 | G | T | 73.2% | 2767.5 / inf | 1387 | S12S (TCG→TCT) | yafL | putative lipoprotein and C40 family peptidase |
| * | CP009273 | 360,752 | 0 | A | G | 70.4% | 1829.4 / inf | 1090 | V331A (GTG→GCG) | lacI | DNA‑binding transcriptional repressor |
| * | CP009273 | 372,858 | 0 | G | A | 64.4% | 592.0 / inf | 839 | intergenic (+91/+133) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| * | CP009273 | 372,863 | 0 | C | T | 61.4% | 343.9 / inf | 807 | intergenic (+96/+128) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| * | CP009273 | 297,897 | 0 | C | T | 61.0% | 1659.2 / inf | 1494 | E130K (GAG→AAG) | paoA | PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit |
| * | CP009273 | 309,254 | 0 | G | A | 54.9% | 702.1 / inf | 1188 | intergenic (‑301/+173) | ykgR/ykgP | uncharacterized protein/pseudogene, oxidoreductase family |
| * | CP009273 | 372,881 | 0 | C | T | 51.7% | 363.5 / inf | 660 | intergenic (+114/+110) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| * | CP009273 | 372,879 | 0 | G | T | 51.7% | 395.3 / inf | 663 | intergenic (+112/+112) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| * | CP009273 | 580,793 | 0 | G | C | 47.2% | 132.5 / inf | 502 | G99G (GGC→GGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,796 | 0 | A | C | 46.9% | 98.2 / inf | 503 | G98G (GGT→GGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,784 | 0 | G | A | 46.8% | 54.7 / inf | 507 | V102V (GTC→GTT) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,805 | 0 | G | A | 46.8% | 104.7 / inf | 507 | G95G (GGC→GGT) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,807 | 0 | C | T | 46.6% | 98.2 / inf | 509 | G95S (GGC→AGC) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,799 | 0 | T | C | 46.5% | 241.3 / inf | 511 | R97R (CGA→CGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,802 | 0 | G | A | 46.5% | 73.9 / inf | 509 | S96S (AGC→AGT) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,806 | 0 | C | T | 46.2% | 119.2 / inf | 509 | G95D (GGC→GAC) ‡ | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,748 | 0 | G | T | 44.8% | 248.0 / inf | 554 | T114T (ACC→ACA) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 580,814 | 0 | T | G | 44.3% | 260.3 / inf | 535 | T92T (ACA→ACC) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| * | CP009273 | 372,887 | 1 | . | T | 43.8% | 1073.9 / inf | 555 | intergenic (+120/+104) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| * | CP009273 | 580,760 | 0 | A | C | 43.5% | 263.5 / inf | 516 | S110R (AGT→AGG) | ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) |
| Marginal new junction evidence (lowest skew 10 of 134 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 1203246 = | 104 (0.280) | 173 (0.520) | 108/266 | 3.3 | 65.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 94 (0.280) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 240616 = | NA (NA) | 361 (1.030) +ACTTCGCCCA |
73/278 | 9.3 | NA | noncoding (1/135 nt) | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | CP009273 | 753859 = | NA (NA) | coding (715/717 nt) | sdhB | succinate dehydrogenase, FeS subunit | |||||
| * | ? | CP009273 | = 108117 | NA (NA) | 232 (0.690) +GTTTATGGGCGAAGT |
44/268 | 15.9 | NA | intergenic (+197/+19) | mutT/yacG | nucleoside triphosphate pyrophosphohydrolase, marked preference for dGTP/DNA gyrase inhibitor |
| ? | CP009273 | 240616 = | NA (NA) | noncoding (1/135 nt) | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | CP009273 | 240621 = | NA (NA) | 140 (0.380) +T |
38/296 | 19.9 | NA | noncoding (6/135 nt) | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | CP009273 | = 372947 | NA (NA) | noncoding (157/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 921313 = | 316 (0.840) | 30 (0.120) | 12/206 | 25.4 | 16.4% | intergenic (+317/+27) | clpA/serW | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser |
| ? | CP009273 | = 1092631 | 89 (0.350) | intergenic (+346/+390) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | CP009273 | = 776472 | 195 (0.520) | 20 (0.070) | 13/224 | 26.3 | 11.4% | intergenic (+98/‑52) | lysW/valZ | tRNA‑Lys/tRNA‑Val |
| ? | CP009273 | 777265 = | 164 (0.580) | intergenic (+157/‑276) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
| * | ? | CP009273 | = 370395 | 1689 (4.510) | 18 (0.050) | 17/264 | 27.0 | 1.2% | noncoding (10/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 370800 = | 1476 (4.460) | noncoding (415/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | CP009273 | = 244028 | NA (NA) | 16 (0.050) | 15/258 | 27.8 | NA | noncoding (84/84 nt) | REP18 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP18 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | CP009273 | 244670 = | NA (NA) | noncoding (37/188 nt) | REP19 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP19 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | = 4285798 | 273 (0.730) | 9 (0.030) | 9/220 | 28.9 | 3.7% | noncoding (76/530 nt) | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 4286251 = | 263 (0.950) | noncoding (529/530 nt) | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | RIP321 (repetitive extragenic palindromic) element; contains 9 REP sequences | |||||
| * | ? | CP009273 | = 776778 | 203 (0.540) | 17 (0.050) | 13/258 | 29.1 | 8.8% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | CP009273 | 777111 = | 176 (0.540) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||