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 47 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,671,531 | 0 | G | T | 35.6% | 119.5 / 12.0 | 87 | E103* (GAG→TAG) | hcaB | 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase |
| * | NC_000913 | 3,911,533 | 0 | C | A | 34.5% | 218.9 / 16.1 | 139 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,351,463 | 0 | C | A | 34.3% | 97.2 / 13.3 | 70 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 3,741,871 | 0 | G | T | 31.1% | 156.4 / 14.0 | 90 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 2,990,480 | 0 | C | A | 31.0% | 276.7 / 17.5 | 158 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 834,674 | 0 | C | A | 30.5% | 174.8 / 10.3 | 95 | L535L (CTC→CTA) | dinG | ATP‑dependent DNA helicase DinG |
| * | NC_000913 | 12,152 | 0 | G | T | 30.4% | 152.8 / 13.1 | 102 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 1,812,509 | 0 | G | T | 30.4% | 258.4 / 13.2 | 135 | L208L (CTC→CTA) | ydjO | protein YdjO |
| * | NC_000913 | 4,096,422 | 0 | C | A | 30.2% | 208.6 / 12.3 | 119 | E343* (GAG→TAG) | rhaB | rhamnulokinase |
| * | NC_000913 | 4,360,965 | 0 | C | A | 29.1% | 363.6 / 22.6 | 175 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 4,136,467 | 0 | A | C | 29.1% | 151.4 / 10.9 | 79 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 1,423,794 | 0 | C | A | 28.7% | 300.3 / 11.2 | 160 | H5N (CAT→AAT) | trkG | K(+) transporter TrkG |
| * | NC_000913 | 1,756,353 | 0 | C | A | 28.5% | 223.8 / 13.9 | 130 | S219Y (TCC→TAC) | pykF | pyruvate kinase 1 |
| * | NC_000913 | 3,768,435 | 0 | C | A | 28.3% | 377.9 / 15.5 | 194 | Q87K (CAG→AAG) | yibG | tetratricopeptide‑like domain‑containing protein YibG |
| * | NC_000913 | 952,453 | 0 | G | T | 28.3% | 214.7 / 10.2 | 120 | P368T (CCG→ACG) | pflB | pyruvate formate‑lyase |
| * | NC_000913 | 2,477,265 | 0 | A | C | 28.3% | 172.7 / 16.3 | 99 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,767,445 | 0 | C | A | 27.9% | 172.7 / 16.0 | 86 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,185,850 | 0 | G | T | 27.8% | 254.7 / 15.0 | 126 | intergenic (‑54/‑67) | rcnR/rcnA | DNA‑binding transcriptional repressor RcnR/Ni(2(+))/Co(2(+)) exporter |
| * | NC_000913 | 1,097,118 | 0 | C | A | 27.5% | 54.5 / 28.1 | 40 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 710,830 | 0 | G | T | 27.3% | 249.4 / 13.0 | 139 | intergenic (‑105/+105) | uof/fldA | RyhB‑regulated fur leader peptide/flavodoxin 1 |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 696469 | 102 (0.940) | 18 (0.190) +36 bp |
13/518 | 4.8 | 18.4% | noncoding (36/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696941 = | 80 (0.740) | intergenic (‑2/+22) | glnU/leuW | tRNA‑Gln/tRNA‑Leu | |||||
| * | ? | NC_000913 | = 781322 | 66 (0.610) | 11 (0.120) | 9/512 | 6.0 | 14.1% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 77 (0.820) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 2357730 | 127 (1.170) | 8 (0.090) | 8/510 | 6.4 | 7.7% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 82 (0.880) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 4094350 | 67 (0.620) | 9 (0.100) | 7/508 | 6.8 | 13.6% | intergenic (‑78/+373) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| ? | NC_000913 | 4094719 = | 57 (0.610) | intergenic (‑447/+4) | rhaD/rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 1286906 | 70 (0.650) | 11 (0.110) | 8/550 | 6.8 | 14.5% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 64 (0.630) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | 781577 = | 71 (0.660) | 15 (0.140) +GAAG |
8/582 | 7.1 | 15.5% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 95 (0.880) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 271761 | NA (NA) | 10 (0.090) | 8/584 | 7.1 | 58.9% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 4640419 | 7 (0.070) | coding (18/141 nt) | yjjY | uncharacterized protein YjjY | |||||
| * | ? | NC_000913 | = 2904225 | 92 (0.850) | 7 (0.070) | 6/530 | 7.4 | 6.5% | intergenic (+851/+522) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| ? | NC_000913 | 2904409 = | 119 (1.220) | intergenic (+1035/+338) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE | |||||
| * | ? | NC_000913 | = 3651580 | 142 (1.310) | 8 (0.070) | 7/590 | 7.6 | 5.3% | pseudogene (290/746 nt) | yhiS | putative uncharacterized protein YhiS |
| ? | NC_000913 | 3652036 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 696506 | 115 (1.060) | 5 (0.050) +45 bp |
5/500 | 7.6 | 5.4% | intergenic (‑2/+36) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 697057 = | 91 (0.840) | noncoding (77/77 nt) | metT | tRNA‑Met | |||||