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 | 3,918,057 | 0 | C | A | 55.6% | 4.4 / 24.4 | 40 | V69L (GTA→TTA) ‡ | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 3,918,075 | 0 | G | T | 53.6% | 6.1 / 22.8 | 30 | L63I (CTA→ATA) | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 3,918,067 | 0 | G | T | 53.1% | 7.7 / 24.6 | 32 | T65T (ACC→ACA) | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 3,175,703 | 0 | G | C | 52.4% | ‑6.4 / 14.1 | 22 | noncoding (1216/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| * | BS168_reference_genome | 3,584,556 | 0 | T | A | 45.7% | 16.2 / 18.3 | 35 | I167F (ATT→TTT) | hisA | phosphoribosylformimino‑5‑aminoimidazole carboxamide ribotide isomerase |
| * | BS168_reference_genome | 3,918,051 | 0 | A | T | 42.0% | 18.8 / 21.9 | 51 | Y71N (TAC→AAC) ‡ | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 911,959 | 0 | T | G | 41.7% | 9.8 / 13.9 | 24 | intergenic (+31/+5) | icaC/yfiR | acetyl‑glucosamine metabolite exporter component involved in biofilm formation/transcriptional regulator (TetR/AcrR family) |
| * | BS168_reference_genome | 3,918,050 | 0 | T | G | 41.2% | 29.0 / 20.8 | 51 | Y71S (TAC→TCC) ‡ | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 194,891 | 0 | G | C | 40.6% | 131.1 / 55.3 | 101 | G15R (GGC→CGC) | sigW | RNA polymerase ECF(extracytoplasmic function)‑type sigma factor W |
| * | BS168_reference_genome | 608,219 | 1 | . | C | 39.5% | 26.1 / 58.3 | 38 | intergenic (‑144/+27) | ydgF/dinB | putative amino acid permease/nuclease inhibitor |
| * | BS168_reference_genome | 3,437,636 | 0 | T | G | 37.8% | 45.7 / 15.6 | 46 | intergenic (‑179/+8) | yvgT/bdbC | putative integral membrane protein/thiol‑disulfide oxidoreductase |
| * | BS168_reference_genome | 608,214 | 1 | . | A | 36.8% | 22.6 / 61.1 | 38 | intergenic (‑139/+32) | ydgF/dinB | putative amino acid permease/nuclease inhibitor |
| * | BS168_reference_genome | 3,333,277 | 0 | T | G | 36.1% | 41.2 / 16.6 | 36 | F39C (TTT→TGT) | pucL | urate oxidase with peroxide reductase N‑terminal domain |
| * | BS168_reference_genome | 1,194,898 | 0 | T | G | 36.0% | 25.3 / 12.4 | 25 | intergenic (+71/‑136) | yitZ/argC | putative transport protein/N‑acetylglutamate gamma‑semialdehyde dehydrogenase |
| * | BS168_reference_genome | 1,023,089 | 0 | A | T | 35.3% | 61.0 / 18.2 | 51 | I287F (ATT→TTT) | yhdF | putative NAD(P)‑dependent dehydrogenase |
| * | BS168_reference_genome | 3,766,734 | 0 | G | T | 33.8% | 94.1 / 17.8 | 71 | Q564K (CAA→AAA) | ureC | urease (alpha subunit) |
| * | BS168_reference_genome | 1,280,481 | 0 | A | C | 33.3% | 52.5 / 13.8 | 36 | L8R (CTA→CGA) | ctaO | minor protoheme IX farnesyltransferase 1 (heme O synthase) |
| * | BS168_reference_genome | 3,484,404 | 0 | C | A | 33.3% | ‑2.1 / 17.3 | 66 | E355* (GAG→TAG) | araE | arabinose‑related compounds permease |
| * | BS168_reference_genome | 3,918,056 | 0 | A | T | 32.6% | 35.4 / 13.2 | 43 | V69E (GTA→GAA) ‡ | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 3,584,560 | 0 | G | C | 32.4% | 38.0 / 13.2 | 34 | V165V (GTC→GTG) | hisA | phosphoribosylformimino‑5‑aminoimidazole carboxamide ribotide isomerase |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | BS168_reference_genome | = 3453354 | 64 (0.830) | 9 (0.140) +GATGTGTATAAGAGACAG |
8/214 | 2.7 | 14.1% | coding (849/2340 nt) | rnr | ribonuclease R |
| ? | BS168_reference_genome | = 3485059 | NA (NA) | coding (408/1395 nt) | araE | arabinose‑related compounds permease | |||||
| * | ? | BS168_reference_genome | 9457 = | 136 (1.770) | 1826 (24.930) | 7/238 | 3.2 | 93.9% | coding (2464/2466 nt) | gyrA | DNA gyrase (subunit A) |
| ? | BS168_reference_genome | 3484075 = | 107 (1.460) | coding (1392/1395 nt) | araE | arabinose‑related compounds permease | |||||
| * | ? | BS168_reference_genome | = 3010366 | 66 (0.860) | 5 (0.000) | 3/240 | 4.5 | 0.20% | coding (233/684 nt) | ytkL | putative metal‑dependent hydrolase |
| ? | pSIJ663_pHT315_araE_xy | 5105 = | 4890 (1.010) | intergenic (+374/–) | ampR/– | –/– | |||||
| * | ? | BS168_reference_genome | 1317177 = | 53 (0.690) | 4 (0.000) | 3/244 | 4.5 | 0.094% | coding (238/258 nt) | yjpA | putative enzyme |
| ? | pSIJ663_pHT315_araE_xy | 860 = | 8424 (1.710) | intergenic (–/‑2118) | –/eryR | –/– | |||||
| * | ? | BS168_reference_genome | = 3924472 | 90 (1.170) | 3 (0.000) | 3/248 | 4.6 | 0.057% | coding (248/1542 nt) | vbfA | acetate Na+‑dependent symporter subunit involved in volatile signal for biofilm formation |
| ? | pSIJ663_pHT315_araE_xy | 1586 = | 10413 (2.080) | intergenic (–/‑1392) | –/eryR | –/– | |||||
| * | ? | BS168_reference_genome | 3682349 = | 111 (1.440) | 3 (0.000) +C |
3/248 | 4.6 | 0.083% | coding (177/1146 nt) | tagB | teichoic acid primase, CDP‑glycerol:N‑acetyl‑beta‑d‑mannosaminyl‑1, 4‑N‑acetyl‑d‑glucosaminyldiphosphoundecaprenyl glycerophosphotransferase |
| ? | pSIJ663_pHT315_araE_xy | = 4859 | 7213 (1.430) | intergenic (+128/–) | ampR/– | –/– | |||||
| * | ? | BS168_reference_genome | = 3484190 | 46 (0.600) | 9 (0.000) | 3/246 | 4.6 | 0.17% | coding (1277/1395 nt) | araE | arabinose‑related compounds permease |
| ? | pSIJ663_pHT315_araE_xy | = 289 | 10775 (2.170) | intergenic (–/‑2689) | –/eryR | –/– | |||||
| * | ? | BS168_reference_genome | 948383 = | NA (NA) | 503 (6.590) | 3/248 | 4.6 | 85.2% | intergenic (+133/‑35) | rrnD‑16S/rrnD‑23S | ribosomal RNA‑16S/ribosomal RNA‑23S |
| ? | BS168_reference_genome | 3176957 = | 88 (1.140) | intergenic (‑39/+129) | rrnB‑23S/rrnB‑16S | ribosomal RNA‑23S/ribosomal RNA‑16S | |||||
| * | ? | BS168_reference_genome | 32141 = | NA (NA) | 59 (0.770) | 3/248 | 4.6 | NA | intergenic (+46/‑36) | trnA‑Ala/rrnA‑23S | tRNA‑Ala/ribosomal RNA‑23S |
| ? | BS168_reference_genome | = 637115 | NA (NA) | intergenic (+128/‑40) | rrnE‑16S/rrnE‑23S | ribosomal RNA‑16S/ribosomal RNA‑23S | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 1838 | 10652 (2.110) | 12 (0.000) | 11/246 | 9.3 | 0.14% | intergenic (–/‑1140) | –/eryR | –/– |
| ? | pSIJ663_pHT315_araE_xy | 2572 = | 6279 (1.270) | intergenic (–/‑406) | –/eryR | –/– | |||||