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 67 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | BS168_reference_genome | 3,174,680 | 0 | A | C | 55.0% | ‑3.6 / 14.5 | 45 | noncoding (2239/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| * | BS168_reference_genome | 515,029 | 0 | T | G | 54.2% | ‑4.7 / 11.8 | 24 | E196A (GAG→GCG) | ydcA | putative rhomboid protease |
| * | BS168_reference_genome | 3,918,057 | 0 | C | A | 51.3% | 19.8 / 41.9 | 39 | V69L (GTA→TTA) ‡ | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 3,175,703 | 0 | G | C | 48.0% | ‑6.4 / 10.6 | 29 | noncoding (1216/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| * | BS168_reference_genome | 515,039 | 0 | G | T | 47.4% | 1.4 / 14.6 | 24 | Q193K (CAA→AAA) | ydcA | putative rhomboid protease |
| * | BS168_reference_genome | 238,232 | 0 | T | G | 43.8% | 23.5 / 24.9 | 48 | pseudogene (217/285 nt) | ybfEc | conserved protein of unknown function (C‑terminal end) |
| * | BS168_reference_genome | 2,318,201 | 0 | C | A | 43.8% | 19.0 / 13.8 | 32 | V415L (GTA→TTA) | pbuX | xanthine permease |
| * | BS168_reference_genome | 608,214 | 1 | . | A | 43.5% | 25.9 / 44.2 | 23 | intergenic (‑139/+32) | ydgF/dinB | putative amino acid permease/nuclease inhibitor |
| * | BS168_reference_genome | 911,959 | 0 | T | G | 40.0% | 18.6 / 17.4 | 35 | intergenic (+31/+5) | icaC/yfiR | acetyl‑glucosamine metabolite exporter component involved in biofilm formation/transcriptional regulator (TetR/AcrR family) |
| * | BS168_reference_genome | 2,003,209 | 0 | T | G | 40.0% | 28.8 / 19.8 | 40 | intergenic (+27/+67) | iseA/trnSL‑Arg1 | inhibitor of DL‑endopeptidases involved in cell‑separation/tRNA‑Arg |
| * | BS168_reference_genome | 3,918,051 | 0 | A | T | 40.0% | 33.2 / 18.7 | 48 | Y71N (TAC→AAC) | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 1,025,107 | 0 | A | C | 39.5% | 22.5 / 13.6 | 38 | E81D (GAA→GAC) | yhdH | putative sodium‑dependent transporter |
| * | BS168_reference_genome | 238,235 | 0 | C | G | 38.6% | 57.5 / 12.8 | 49 | pseudogene (214/285 nt) | ybfEc | conserved protein of unknown function (C‑terminal end) |
| * | BS168_reference_genome | 1,619,277 | 0 | A | C | 37.9% | 16.0 / 14.6 | 29 | K85N (AAA→AAC) | pyrP | uracil permease |
| * | BS168_reference_genome | 614,809 | 0 | T | G | 35.6% | 38.8 / 14.7 | 45 | F390C (TTT→TGT) | ydgK | putative efflux transporter |
| * | BS168_reference_genome | 490,561 | 0 | A | C | 34.6% | 86.2 / 22.1 | 78 | P63P (CCT→CCG) | BSU_04345 | hypothetical protein |
| * | BS168_reference_genome | 3,918,056 | 0 | A | T | 34.2% | 37.8 / 12.3 | 39 | V69E (GTA→GAA) ‡ | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 3,995,588 | 0 | T | G | 34.0% | 45.9 / 14.0 | 51 | F172V (TTT→GTT) | pepT | peptidase T (tripeptidase) |
| * | BS168_reference_genome | 194,891 | 0 | G | C | 33.3% | 94.7 / 20.3 | 54 | G15R (GGC→CGC) | sigW | RNA polymerase ECF(extracytoplasmic function)‑type sigma factor W |
| * | BS168_reference_genome | 2,442,639 | 0 | A | C | 33.3% | 48.6 / 12.9 | 48 | V19G (GTG→GGG) | spoVAB | stage V sporulation protein AB |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | 9457 = | 93 (1.230) | 1307 (18.170) | 4/242 | 5.0 | 93.0% | coding (2464/2466 nt) | gyrA | DNA gyrase (subunit A) |
| ? | BS168_reference_genome | 3484075 = | 109 (1.520) | coding (1392/1395 nt) | araE | arabinose‑related compounds permease | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5614 | 3 (0.000) | 12 (0.000) | 10/248 | 10.3 | 75.2% | intergenic (+883/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9532 = | 5 (0.000) | intergenic (+4801/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 1838 | 7984 (2.060) | 9 (0.000) | 6/250 | 12.0 | 0.15% | intergenic (–/‑1140) | –/eryR | –/– |
| ? | pSIJ663_pHT315_araE_xy | 2572 = | 4527 (1.190) | intergenic (–/‑406) | –/eryR | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | 3854 = | 223 (0.060) | 5 (0.000) +A |
4/252 | 13.1 | 4.3% | intergenic (+139/‑17) | eryR/ampR | –/– |
| ? | pSIJ663_pHT315_araE_xy | = 11568 | 0 (0.000) | intergenic (+6837/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | 1515 = | 8110 (2.090) | 3 (0.000) | 3/248 | 13.7 | 0.047% | intergenic (–/‑1463) | –/eryR | –/– |
| ? | pSIJ663_pHT315_araE_xy | = 1764 | 4848 (1.280) | intergenic (–/‑1214) | –/eryR | –/– | |||||