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 70 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | BS168_reference_genome | 2,003,214 | 0 | A | T | 58.1% | 2.5 / 15.6 | 31 | intergenic (+32/+62) | iseA/trnSL‑Arg1 | inhibitor of DL‑endopeptidases involved in cell‑separation/tRNA‑Arg |
| * | BS168_reference_genome | 608,214 | 1 | . | A | 56.7% | 44.2 / 45.9 | 30 | intergenic (‑139/+32) | ydgF/dinB | putative amino acid permease/nuclease inhibitor |
| * | BS168_reference_genome | 3,918,057 | 0 | C | A | 51.4% | 14.1 / 32.5 | 39 | V69L (GTA→TTA) ‡ | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 1,291,923 | 0 | T | G | 47.1% | 31.8 / 37.5 | 68 | F194V (TTT→GTT) | cypE | cytochrome P450 CYP109B1, monooxygenase |
| * | BS168_reference_genome | 2,003,209 | 0 | T | G | 46.9% | 2.0 / 20.9 | 32 | intergenic (+27/+67) | iseA/trnSL‑Arg1 | inhibitor of DL‑endopeptidases involved in cell‑separation/tRNA‑Arg |
| * | BS168_reference_genome | 3,774,622 | 0 | G | C | 44.7% | 39.8 / 34.6 | 48 | intergenic (‑61/+33) | ywmE/ywmD | conserved protein of unknown function/putative exported protein |
| * | BS168_reference_genome | 238,235 | 0 | C | G | 41.7% | 68.8 / 22.1 | 70 | pseudogene (214/285 nt) | ybfEc | conserved protein of unknown function (C‑terminal end) |
| * | BS168_reference_genome | 1,185,561 | 0 | T | G | 40.6% | 29.6 / 10.2 | 32 | A187A (GCT→GCG) | yitQ | conserved protein of unknown function |
| * | BS168_reference_genome | 3,766,730 | 0 | C | A | 40.0% | 51.7 / 11.7 | 50 | R565I (AGA→ATA) | ureC | urease (alpha subunit) |
| * | BS168_reference_genome | 238,232 | 0 | T | G | 39.7% | 48.1 / 35.9 | 68 | pseudogene (217/285 nt) | ybfEc | conserved protein of unknown function (C‑terminal end) |
| * | BS168_reference_genome | 3,485,004 | 0 | G | T | 38.6% | ‑3.9 / 10.2 | 63 | Q155K (CAG→AAG) | araE | arabinose‑related compounds permease |
| * | BS168_reference_genome | 3,774,621 | 0 | A | C | 37.8% | 55.7 / 13.8 | 47 | intergenic (‑60/+34) | ywmE/ywmD | conserved protein of unknown function/putative exported protein |
| * | BS168_reference_genome | 4,107,409 | 0 | T | G | 37.3% | 46.8 / 14.7 | 59 | K173N (AAA→AAC) | qdoR | transcriptional regulator of qdoI |
| * | BS168_reference_genome | 3,918,056 | 0 | A | T | 36.8% | 37.4 / 10.8 | 39 | V69E (GTA→GAA) ‡ | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 911,959 | 0 | T | G | 36.4% | 30.1 / 12.0 | 33 | intergenic (+31/+5) | icaC/yfiR | acetyl‑glucosamine metabolite exporter component involved in biofilm formation/transcriptional regulator (TetR/AcrR family) |
| * | BS168_reference_genome | 2,620,945 | 0 | C | G | 36.1% | 43.9 / 11.3 | 36 | L77V (CTT→GTT) | yqeW | putative Na+/anion cotransporter |
| * | BS168_reference_genome | 3,333,277 | 0 | T | G | 34.8% | 63.5 / 16.9 | 46 | F39C (TTT→TGT) | pucL | urate oxidase with peroxide reductase N‑terminal domain |
| * | BS168_reference_genome | 3,774,615 | 0 | T | A | 34.8% | 57.1 / 16.9 | 46 | intergenic (‑54/+40) | ywmE/ywmD | conserved protein of unknown function/putative exported protein |
| * | BS168_reference_genome | 463,394 | 0 | C | A | 34.3% | 97.5 / 17.9 | 70 | R50R (CGC→CGA) | yczI | conserved protein of unknown function |
| * | BS168_reference_genome | 1,641,648 | 0 | T | G | 34.2% | 49.6 / 10.2 | 39 | intergenic (+53/‑24) | yloC/remA | conserved protein of unknown function/essential sporulation DNA binding protein; regulator of biofilm formation |
| 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 = | 107 (1.300) | 1134 (14.480) | 4/238 | 5.5 | 91.4% | coding (2464/2466 nt) | gyrA | DNA gyrase (subunit A) |
| ? | BS168_reference_genome | 3484075 = | 112 (1.430) | coding (1392/1395 nt) | araE | arabinose‑related compounds permease | |||||
| * | ? | BS168_reference_genome | = 700631 | 69 (0.840) | 5 (0.000) | 3/244 | 6.0 | 0.14% | coding (400/1296 nt) | purB | adenylosuccinate lyase |
| ? | pSIJ663_pHT315_araE_xy | 673 = | 7321 (2.270) | intergenic (–/‑2305) | –/eryR | –/– | |||||
| * | ? | BS168_reference_genome | = 4128586 | 130 (1.580) | 4 (0.000) +T |
3/248 | 6.1 | 0.23% | coding (468/1926 nt) | fbp | fructose‑1,6‑bisphosphatase |
| ? | pSIJ663_pHT315_araE_xy | = 5098 | 3442 (1.040) | intergenic (+367/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5048 | 3456 (1.050) | 157 (0.050) | 16/248 | 9.1 | 4.1% | intergenic (+317/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 5052 = | 3855 (1.180) | intergenic (+321/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5614 | 7 (0.000) | 15 (0.000) | 13/244 | 9.9 | 68.5% | intergenic (+883/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9532 = | 7 (0.000) | intergenic (+4801/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 1838 | 6854 (2.080) | 9 (0.000) | 8/246 | 11.8 | 0.17% | intergenic (–/‑1140) | –/eryR | –/– |
| ? | pSIJ663_pHT315_araE_xy | 2572 = | 3960 (1.220) | intergenic (–/‑406) | –/eryR | –/– | |||||