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 226 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,429,537 | 0 | G | A | 79.4% | 68.5 / 15.2 | 34 | A163A (GCG→GCA) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,543 | 0 | G | A | 79.4% | 75.4 / 13.8 | 34 | S165S (TCG→TCA) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,462 | 0 | C | T | 79.3% | 60.6 / 12.8 | 30 | A138A (GCC→GCT) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,682 | 0 | T | G | 78.7% | 107.4 / 24.9 | 47 | S212A (TCA→GCA) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,550 | 0 | T | G | 78.4% | 79.4 / 18.4 | 37 | S168A (TCA→GCA) ‡ | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,551 | 0 | C | A | 78.4% | 64.2 / 21.1 | 37 | S168* (TCA→TAA) ‡ | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,692 | 0 | T | A | 78.3% | 108.3 / 36.1 | 46 | L215Q (CTA→CAA) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,111 | 0 | A | C | 77.8% | 108.1 / 23.3 | 45 | T21T (ACA→ACC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,126 | 0 | A | C | 77.8% | 106.6 / 23.2 | 46 | A26A (GCA→GCC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,128 | 0 | A | G | 77.8% | 94.8 / 23.7 | 46 | K27R (AAA→AGA) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,114 | 0 | C | T | 77.3% | 89.6 / 22.4 | 45 | I22I (ATC→ATT) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,702 | 0 | A | C | 77.3% | 87.0 / 20.6 | 44 | A218A (GCA→GCC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,724 | 0 | A | G | 77.3% | 80.1 / 24.6 | 44 | T226A (ACC→GCC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,732 | 0 | G | A | 77.3% | 87.9 / 18.3 | 44 | K228K (AAG→AAA) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,735 | 0 | A | G | 77.3% | 85.3 / 24.1 | 44 | A229A (GCA→GCG) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,741 | 0 | A | G | 77.3% | 84.0 / 24.6 | 44 | E231E (GAA→GAG) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,632 | 0 | G | A | 76.1% | 87.3 / 27.5 | 46 | S195N (AGC→AAC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,069 | 0 | T | A | 75.6% | 96.1 / 35.0 | 41 | G7G (GGT→GGA) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,072 | 0 | A | C | 75.6% | 87.8 / 22.5 | 41 | V8V (GTA→GTC) | stfR | putative prophage side tail fiber protein StfR |
| * | NC_000913 | 1,429,744 | 0 | T | C | 75.6% | 84.3 / 25.4 | 45 | A232A (GCT→GCC) | stfR | putative prophage side tail fiber protein StfR |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 780629 | 99 (1.000) | 9 (0.120) | 9/446 | 3.9 | 12.3% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 55 (0.750) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | = 2466384 | 81 (0.820) | 14 (0.150) | 12/566 | 4.0 | 12.9% | intergenic (+1/‑161) | argW/intS | tRNA‑Arg/prophage CPS‑53 integrase |
| ? | NC_000913 | 2476600 = | 112 (1.200) | intergenic (+90/+94) | torI/dsdC | prophage CPS‑53 recombination directionality factor and response regulator inhibitor/DNA‑binding transcriptional dual regulator DsdC | |||||
| * | ? | NC_000913 | = 2653419 | 81 (0.820) | 12 (0.130) | 10/548 | 4.4 | 13.7% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 77 (0.850) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 3648146 | 144 (1.460) | 9 (0.110) | 7/482 | 4.8 | 7.1% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 118 (1.480) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 4606166 | 84 (0.850) | 4 (0.060) | 3/420 | 5.9 | 7.1% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 45 (0.650) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2947467 | 81 (0.820) | 3 (0.040) | 3/432 | 6.0 | 4.7% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 62 (0.870) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 696741 | 52 (0.530) | 4 (0.050) | 3/442 | 6.1 | 8.0% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 54 (0.740) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 2357690 | 91 (0.920) | 4 (0.040) | 4/548 | 6.4 | 4.6% | coding (787/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357874 = | 83 (0.920) | intergenic (+71/+168) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 2357730 | 94 (0.950) | 3 (0.040) | 3/518 | 6.7 | 3.5% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 84 (0.980) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | 3270072 = | 55 (0.560) | 3 (0.030) +25 bp |
3/548 | 6.9 | 3.5% | intergenic (+470/+144) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| ? | NC_000913 | 4137788 = | 128 (1.300) | intergenic (‑131/+144) | yijF/gldA | DUF1287 domain‑containing protein YijF/L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase | |||||