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 119 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | BS168_reference_genome | 2,003,209 | 0 | T | G | 63.0% | 7.2 / 45.8 | 54 | intergenic (+27/+67) | iseA/trnSL‑Arg1 | inhibitor of DL‑endopeptidases involved in cell‑separation/tRNA‑Arg |
| * | BS168_reference_genome | 3,174,680 | 0 | A | C | 58.7% | ‑4.7 / 17.5 | 50 | noncoding (2239/2928 nt) | rrnB‑23S | ribosomal RNA‑23S |
| * | BS168_reference_genome | 238,235 | 0 | C | G | 47.0% | 51.2 / 32.8 | 79 | pseudogene (214/285 nt) | ybfEc | conserved protein of unknown function (C‑terminal end) |
| * | BS168_reference_genome | 911,962 | 0 | C | G | 46.4% | 28.7 / 11.1 | 30 | intergenic (+34/+2) | icaC/yfiR | acetyl‑glucosamine metabolite exporter component involved in biofilm formation/transcriptional regulator (TetR/AcrR family) |
| * | BS168_reference_genome | 2,003,224 | 0 | C | G | 46.4% | 42.6 / 30.6 | 58 | intergenic (+42/+52) | iseA/trnSL‑Arg1 | inhibitor of DL‑endopeptidases involved in cell‑separation/tRNA‑Arg |
| * | BS168_reference_genome | 2,003,214 | 0 | A | T | 46.3% | ‑1.8 / 36.2 | 54 | intergenic (+32/+62) | iseA/trnSL‑Arg1 | inhibitor of DL‑endopeptidases involved in cell‑separation/tRNA‑Arg |
| * | BS168_reference_genome | 608,214 | 1 | . | A | 45.7% | 42.1 / 73.2 | 35 | intergenic (‑139/+32) | ydgF/dinB | putative amino acid permease/nuclease inhibitor |
| * | BS168_reference_genome | 2,003,218 | 0 | G | T | 44.2% | 32.0 / 22.9 | 52 | intergenic (+36/+58) | iseA/trnSL‑Arg1 | inhibitor of DL‑endopeptidases involved in cell‑separation/tRNA‑Arg |
| * | BS168_reference_genome | 608,219 | 1 | . | C | 42.9% | 11.4 / 62.1 | 35 | intergenic (‑144/+27) | ydgF/dinB | putative amino acid permease/nuclease inhibitor |
| * | BS168_reference_genome | 3,918,056 | 0 | A | T | 36.8% | 32.2 / 11.0 | 38 | V69E (GTA→GAA) | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 470,898 | 0 | G | T | 36.7% | 63.4 / 11.0 | 55 | V491V (GTG→GTT) | ydaB | putative acyl‑CoA ligase |
| * | BS168_reference_genome | 238,232 | 0 | T | G | 36.4% | 46.3 / 34.1 | 77 | pseudogene (217/285 nt) | ybfEc | conserved protein of unknown function (C‑terminal end) |
| * | BS168_reference_genome | 1,140,541 | 0 | A | C | 35.7% | 72.7 / 20.6 | 70 | K245N (AAA→AAC) | addA | ATP‑dependent deoxyribonuclease (subunit A) |
| * | BS168_reference_genome | 1,176,041 | 0 | C | G | 35.1% | 107.2 / 14.9 | 64 | E405Q (GAA→CAA) | yitG | putative efflux transporter |
| * | BS168_reference_genome | 2,628,807 | 0 | C | A | 35.0% | 60.9 / 10.6 | 40 | S277S (TCG→TCT) | hrcA | transcriptional regulator of heat‑shock genes |
| * | BS168_reference_genome | 3,658,828 | 0 | G | T | 33.9% | 54.4 / 11.7 | 68 | pseudogene (65/486 nt) | tuaAn | putative undecaprenyl‑phosphate N‑acetylgalactosaminyl‑1‑phosphate transferase; N‑terminal part of TuaA |
| * | BS168_reference_genome | 1,291,923 | 0 | T | G | 33.7% | 116.8 / 30.0 | 98 | F194V (TTT→GTT) | cypE | cytochrome P450 CYP109B1, monooxygenase |
| * | BS168_reference_genome | 3,526,847 | 0 | C | G | 33.3% | 43.2 / 17.2 | 37 | G453R (GGC→CGC) | epsC | putative UDP‑sugar epimerase involved in biofilm matrix formation |
| * | BS168_reference_genome | 3,918,051 | 0 | A | T | 33.3% | 37.7 / 11.6 | 40 | Y71N (TAC→AAC) | qoxA | cytochrome aa3‑600 quinol oxidase (subunit II) |
| * | BS168_reference_genome | 1,176,050 | 0 | C | G | 32.8% | 114.5 / 14.7 | 66 | E402Q (GAA→CAA) | yitG | putative efflux transporter |
| 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 = | 142 (1.440) | 3330 (35.450) | 8/240 | 4.7 | 96.4% | coding (2464/2466 nt) | gyrA | DNA gyrase (subunit A) |
| ? | BS168_reference_genome | 3484075 = | 111 (1.180) | coding (1392/1395 nt) | araE | arabinose‑related compounds permease | |||||
| * | ? | BS168_reference_genome | 68562 = | 143 (1.450) | 13 (0.000) | 4/248 | 6.4 | 0.24% | coding (48/636 nt) | spcQ | membrane protein of the forespore |
| ? | pSIJ663_pHT315_araE_xy | = 5354 | 10824 (1.120) | intergenic (+623/–) | ampR/– | –/– | |||||
| * | ? | BS168_reference_genome | 1979085 = | 92 (0.930) | 3 (0.030) | 3/242 | 6.8 | 3.3% | coding (3464/7668 nt) | ppsC | non‑ribosomal plipastatin synthetase C involved in synthesis of plipastatin |
| ? | BS168_reference_genome | 3484366 = | NA (NA) | coding (1101/1395 nt) | araE | arabinose‑related compounds permease | |||||
| * | ? | BS168_reference_genome | 3448258 = | 100 (1.010) | 3 (0.000) | 3/250 | 7.0 | 0.047% | intergenic (‑126/+37) | yvaC/yvaD | putative integral inner membrane protein/putative integral inner membrane protein |
| ? | pSIJ663_pHT315_araE_xy | 3145 = | 12721 (1.310) | coding (168/738 nt) | eryR | ||||||
| * | ? | pSIJ663_pHT315_araE_xy | = 4968 | 13945 (1.530) | 420 (0.040) +GTTT |
8/226 | 13.0 | 2.8% | intergenic (+237/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 4969 = | 15471 (1.580) | intergenic (+238/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | 5140 = | 16027 (1.630) | 35 (0.000) | 8/242 | 13.5 | 0.23% | intergenic (+409/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | = 5136 | 15461 (1.640) | intergenic (+405/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 5614 | 12 (0.000) | 8 (0.000) | 7/246 | 14.1 | 47.5% | intergenic (+883/–) | ampR/– | –/– |
| ? | pSIJ663_pHT315_araE_xy | 9532 = | 6 (0.000) | intergenic (+4801/–) | ampR/– | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 1838 | 20868 (2.130) | 8 (0.000) | 6/248 | 14.7 | 0.050% | intergenic (–/‑1140) | –/eryR | –/– |
| ? | pSIJ663_pHT315_araE_xy | 2572 = | 11472 (1.190) | intergenic (–/‑406) | –/eryR | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | 1737 = | 15834 (1.620) | 3 (0.000) | 3/242 | 16.4 | 0.020% | intergenic (–/‑1241) | –/eryR | –/– |
| ? | pSIJ663_pHT315_araE_xy | = 1733 | 14551 (1.550) | intergenic (–/‑1245) | –/eryR | –/– | |||||
| * | ? | pSIJ663_pHT315_araE_xy | = 3695 | 9379 (0.960) | 4 (0.000) | 3/250 | 16.7 | 0.043% | coding (718/738 nt) | eryR | |
| ? | pSIJ663_pHT315_araE_xy | 3701 = | 9492 (0.980) | coding (724/738 nt) | eryR | ||||||