mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 375 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,999,525 | 0 | G | T | 79.8% | 160.8 / 35.3 | 79 | Q123K (CAA→AAA) | actS | amidase activator |
| * | NC_000913 | 2,934,489 | 0 | G | T | 79.5% | 90.6 / 16.8 | 45 | M85I (ATG→ATT) | fucP | L‑fucose:H(+) symporter |
| * | NC_000913 | 2,594,898 | 0 | G | T | 78.7% | 222.9 / 67.4 | 109 | A321E (GCG→GAG) | tmcA | tRNA(Met) cytidine acetyltransferase |
| * | NC_000913 | 1,800,345 | 0 | G | T | 78.6% | 179.5 / 50.2 | 84 | F98L (TTC→TTA) | infC | translation initiation factor IF‑3 |
| * | NC_000913 | 2,698,494 | 0 | C | A | 78.3% | 183.3 / 49.6 | 98 | Q19H (CAG→CAT) | pgpC | phosphatidylglycerophosphatase C |
| * | NC_000913 | 2,834,173 | 0 | G | T | 78.1% | 203.3 / 37.6 | 107 | A88S (GCC→TCC) | norW | NADH:flavorubredoxin reductase |
| * | NC_000913 | 2,632,733 | 0 | G | T | 76.8% | 198.0 / 66.8 | 108 | G446G (GGC→GGA) | guaB | inosine 5'‑monophosphate dehydrogenase |
| * | NC_000913 | 3,185,531 | 0 | C | A | 76.1% | 120.6 / 55.0 | 67 | P40T (CCA→ACA) | ygiL | putative fimbrial protein YgiL |
| * | NC_000913 | 130,995 | 0 | G | T | 76.1% | 274.3 / 75.1 | 140 | P89H (CCC→CAC) | yacH | DUF3300 domain‑containing protein YacH |
| * | NC_000913 | 3,872,186 | 0 | G | T | 75.8% | 166.9 / 60.5 | 99 | I271I (ATC→ATA) | dgoD | D‑galactonate dehydratase |
| * | NC_000913 | 3,631,889 | 0 | C | A | 75.6% | 73.7 / 32.2 | 45 | L234F (TTG→TTT) | yhiJ | DUF4049 domain‑containing protein YhiJ |
| * | NC_000913 | 1,907,163 | 0 | C | A | 75.5% | 180.0 / 69.4 | 94 | intergenic (‑103/+63) | rlmA/cspC | 23S rRNA m(1)G745 methyltransferase/transcription antiterminator and regulator of mRNA stability CspC |
| * | NC_000913 | 3,746,314 | 0 | C | A | 75.5% | 147.7 / 64.0 | 94 | A74E (GCG→GAG) | yiaO | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ periplasmic binding protein |
| * | NC_000913 | 578,831 | 0 | T | C | 75.3% | 322.3 / 117.2 | 170 | T21T (ACA→ACG) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 578,729 | 0 | A | G | 74.8% | 320.9 / 107.9 | 161 | A55A (GCT→GCC) | borD | prophage lipoprotein BorD |
| * | NC_000913 | 2,980,479 | 0 | G | T | 73.8% | 146.6 / 51.8 | 84 | R53S (CGT→AGT) | ygeA | amino acid racemase YgeA |
| * | NC_000913 | 2,829,007 | 0 | G | T | 73.6% | 168.7 / 63.0 | 91 | intergenic (+27/‑40) | gutM/srlR | DNA‑binding transcriptional activator GutM/DNA‑binding transcriptional repressor SrlR |
| * | NC_000913 | 3,891,397 | 1 | . | A | 73.6% | 236.7 / 79.8 | 88 | coding (1162/1248 nt) | tnaB | tryptophan:H(+) symporter TnaB |
| * | NC_000913 | 2,800,797 | 0 | C | A | 73.6% | 190.3 / 91.2 | 121 | G25G (GGC→GGA) | nrdH | glutaredoxin‑like protein NrdH |
| * | NC_000913 | 4,321,258 | 0 | C | A | 73.4% | 306.0 / 150.5 | 188 | G147* (GGA→TGA) | phnG | carbon‑phosphorus lyase core complex subunit PhnG |
| Marginal new junction evidence (lowest skew 10 of 42 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 764398 = | 235 (1.930) | 38 (0.380) +43 bp |
26/394 | 2.1 | 13.6% | coding (219/870 nt) | sucD | succinyl‑CoA synthetase subunit alpha |
| ? | NC_000913 | = 1429224 | 351 (2.880) | coding (176/3363 nt) | stfR | putative prophage side tail fiber protein StfR | |||||
| * | ? | NC_000913 | = 4365924 | 103 (0.850) | 22 (0.180) | 22/480 | 3.0 | 17.6% | coding (850/1302 nt) | dcuA | C4‑dicarboxylate transporter DcuA |
| ? | NC_000913 | = 4499511 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1577784 = | 112 (0.920) | 28 (0.230) | 20/478 | 3.2 | 20.1% | coding (1559/1686 nt) | yddA | ABC transporter family protein YddA |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 687851 = | NA (NA) | 19 (0.160) | 17/480 | 3.5 | 22.1% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 738765 = | 67 (0.550) | coding (674/762 nt) | ybfD | H repeat‑associated putative transposase YbfD | |||||
| * | ? | NC_000913 | = 3991039 | 57 (0.470) | 16 (0.130) | 16/480 | 3.7 | 21.9% | intergenic (‑273/‑114) | hemC/cyaA | hydroxymethylbilane synthase/adenylate cyclase |
| ? | NC_000913 | = 4508679 | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 17 (0.140) | 16/480 | 3.7 | 13.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 678027 | 108 (0.890) | coding (613/1428 nt) | djlB | J domain‑containing protein DjlB | |||||
| * | ? | NC_000913 | 3365556 = | NA (NA) | 16 (0.130) | 14/480 | 4.0 | 19.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3413954 = | 67 (0.550) | coding (91/1158 nt) | acrE | multidrug efflux pump membrane fusion lipoprotein AcrE | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 14 (0.110) | 14/480 | 4.0 | 20.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3888549 | 55 (0.450) | intergenic (+40/‑181) | tnaC/tnaA | tnaAB operon leader peptide/tryptophanase | |||||
| * | ? | NC_000913 | = 891858 | 49 (0.400) | 14 (0.110) | 13/480 | 4.1 | 22.2% | coding (675/723 nt) | nfsA | NADPH‑dependent nitro/quinone reductase NfsA |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 4542682 = | 64 (0.530) | 13 (0.110) | 12/462 | 4.2 | 14.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 88 (0.750) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||