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 55 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 58,065 | 0 | C | A | 46.0% | 75.3 / 27.9 | 74 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 40.7% | 166.2 / 36.1 | 145 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 377,407 | 0 | C | T | 37.5% | 69.3 / 75.9 | 72 | intergenic (+96/+128) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 1,097,118 | 0 | C | A | 36.7% | 23.8 / 42.0 | 49 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 1,286,874 | 0 | G | A | 35.7% | 75.4 / 24.9 | 56 | A56T (GCT→ACT) | ychS | putative uncharacterized protein YchS |
| * | NC_000913 | 377,402 | 0 | G | A | 34.6% | 90.4 / 68.1 | 78 | intergenic (+91/+133) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 320,845 | 0 | C | A | 34.5% | 173.8 / 20.8 | 142 | R207R (CGG→AGG) | rclR | DNA‑binding transcriptional activator RclR |
| * | NC_000913 | 710,830 | 0 | G | T | 34.1% | 138.4 / 18.7 | 91 | intergenic (‑105/+105) | uof/fldA | RyhB‑regulated fur leader peptide/flavodoxin 1 |
| * | NC_000913 | 377,423 | 0 | G | T | 33.3% | 99.8 / 50.3 | 69 | intergenic (+112/+112) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 2,990,480 | 0 | C | A | 33.1% | 205.5 / 15.6 | 130 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 3,054,894 | 0 | G | T | 32.4% | 87.3 / 17.6 | 71 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,722,838 | 0 | G | T | 32.0% | 159.0 / 12.5 | 103 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 377,431 | 1 | . | T | 31.5% | 154.4 / 114.3 | 73 | intergenic (+120/+104) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 377,432 | 0 | C | G | 31.5% | 122.3 / 75.0 | 73 | intergenic (+121/+103) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 3,054,886 | 0 | G | T | 31.2% | 100.4 / 25.0 | 80 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,812,509 | 0 | G | T | 31.2% | 196.9 / 22.6 | 109 | L208L (CTC→CTA) | ydjO | protein YdjO |
| * | NC_000913 | 377,425 | 0 | C | T | 31.1% | 104.5 / 61.1 | 74 | intergenic (+114/+110) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| * | NC_000913 | 1,390,607 | 0 | C | A | 30.5% | 166.8 / 15.3 | 105 | intergenic (‑9/+73) | mpaA/ymjC | murein tripeptide amidase A/putative uncharacterized protein YmjC |
| * | NC_000913 | 3,181,243 | 0 | G | T | 29.0% | 185.2 / 10.4 | 100 | E275* (GAG→TAG) | ygiC | putative acid‑‑amine ligase YgiC |
| * | NC_000913 | 782,194 | 0 | T | G | 28.4% | 140.5 / 12.0 | 97 | L37R (CTA→CGA) | nadA | quinolinate synthase |
| Marginal new junction evidence (lowest skew 10 of 39 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 781222 | 58 (0.680) | 17 (0.270) | 13/438 | 3.0 | 27.0% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 49 (0.770) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 2653419 | 78 (0.910) | 18 (0.230) | 14/540 | 3.7 | 20.8% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 66 (0.840) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 696469 | 75 (0.870) | 20 (0.240) +TAGAAT |
13/578 | 4.2 | 25.6% | noncoding (36/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696802 = | 44 (0.510) | noncoding (29/75 nt) | glnW | tRNA‑Gln | |||||
| * | ? | NC_000913 | = 3648146 | 115 (1.340) | 11 (0.160) | 9/474 | 4.5 | 10.8% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 89 (1.290) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | 1978159 = | 103 (1.200) | 16 (0.190) | 8/590 | 5.8 | 13.5% | coding (39/351 nt) | flhD | DNA‑binding transcriptional dual regulator FlhD |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 2357730 | 114 (1.330) | 7 (0.090) | 6/510 | 5.9 | 6.8% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 92 (1.240) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 3621836 | NA (NA) | 6 (0.070) | 6/566 | 6.4 | 86.2% | coding (2645/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3622017 = | 1 (0.010) | coding (2826/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 732239 | 55 (0.640) | 6 (0.070) | 6/566 | 6.4 | 18.2% | coding (2657/4194 nt) | rhsC | rhs element protein RhsC |
| ? | NC_000913 | 3622029 = | 1 (0.010) | coding (2838/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 524357 | 35 (0.410) | 6 (0.070) | 6/562 | 6.4 | 15.1% | coding (1097/4281 nt) | rhsD | protein RhsD |
| ? | NC_000913 | 524805 = | 34 (0.420) | coding (1545/4281 nt) | rhsD | protein RhsD | |||||
| * | ? | NC_000913 | = 2818256 | 50 (0.580) | 6 (0.070) +A |
6/588 | 6.6 | 8.2% | noncoding (19/77 nt) | argY | tRNA‑Arg |
| ? | NC_000913 | 2818533 = | 84 (0.980) | noncoding (17/77 nt) | argV | tRNA‑Arg | |||||