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 45 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,208,132 | 0 | G | A | 71.2% | 209.9 / 154.5 | 179 | intergenic (‑600/‑15) | purH/rrsE | bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA |
| * | NC_000913 | 3,943,452 | 0 | G | A | 50.0% | ‑3.9 / 83.7 | 50 | noncoding (18/76 nt) | gltU | tRNA‑Glu |
| * | NC_000913 | 1,097,118 | 0 | C | A | 46.7% | 10.5 / 51.4 | 45 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,477,265 | 0 | A | C | 40.8% | 133.2 / 33.9 | 98 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,943,634 | 0 | A | G | 40.4% | 101.1 / 185.0 | 149 | intergenic (+124/‑70) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA |
| * | NC_000913 | 3,054,886 | 0 | G | T | 38.3% | 153.9 / 39.8 | 108 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 58,065 | 0 | C | A | 35.0% | 159.9 / 18.6 | 97 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,334,966 | 0 | A | C | 34.4% | 224.6 / 36.7 | 163 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 1,097,158 | 0 | C | T | 34.2% | 29.3 / 29.8 | 38 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 3,054,894 | 0 | G | T | 30.4% | 150.1 / 29.9 | 103 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,911,533 | 0 | C | A | 30.1% | 284.0 / 22.7 | 153 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,502,772 | 0 | G | A | 29.8% | 146.3 / 28.0 | 94 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 1,502,770 | 0 | T | C | 29.5% | 156.9 / 28.7 | 95 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 3,741,871 | 0 | G | T | 28.9% | 252.7 / 28.4 | 135 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 4,209,791 | 0 | G | A | 28.6% | 310.3 / 235.4 | 252 | noncoding (18/76 nt) | gltV | tRNA‑Glu |
| * | NC_000913 | 2,767,449 | 0 | C | A | 27.8% | 296.6 / 12.6 | 133 | intergenic (+94/‑261) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,922,815 | 0 | C | A | 27.4% | 170.1 / 29.2 | 106 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 161,559 | 0 | G | A | 27.0% | 152.8 / 12.3 | 74 | S158L (TCG→TTG) | thpR | RNA 2',3'‑cyclic phosphodiesterase |
| * | NC_000913 | 4,360,965 | 0 | C | A | 26.9% | 364.3 / 31.1 | 175 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 847,955 | 0 | G | A | 26.5% | 215.5 / 35.6 | 123 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4606166 | 93 (0.900) | 8 (0.110) | 8/420 | 5.2 | 10.0% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 79 (1.090) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2357730 | 122 (1.190) | 7 (0.080) | 7/518 | 6.6 | 6.4% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 98 (1.100) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 1287329 | 72 (0.700) | 4 (0.050) | 4/424 | 7.0 | 8.7% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 33 (0.450) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 696741 | 80 (0.780) | 4 (0.050) | 4/442 | 7.2 | 6.1% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 64 (0.840) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 1286906 | 54 (0.530) | 8 (0.080) | 5/558 | 7.9 | 13.9% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 49 (0.510) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2304500 | 48 (0.470) | 3 (0.030) | 3/506 | 8.5 | 6.4% | intergenic (+107/+608) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| ? | NC_000913 | 2305066 = | 47 (0.540) | intergenic (+673/+42) | eco/mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase | |||||
| * | ? | NC_000913 | = 2878034 | 73 (0.710) | 4 (0.040) | 3/540 | 8.9 | 5.2% | intergenic (+416/+535) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| ? | NC_000913 | 2878281 = | 80 (0.860) | intergenic (+663/+288) | iap/cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 | |||||
| * | ? | NC_000913 | = 2653520 | 99 (0.960) | 4 (0.040) +TTATTATCGACAC |
3/572 | 9.2 | 4.1% | intergenic (‑65/‑335) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA |
| ? | NC_000913 | 2653856 = | 96 (0.930) | noncoding (2/304 nt) | ryfA | small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 696433 | 118 (1.150) | 3 (0.030) +C |
3/596 | 9.4 | 2.8% | noncoding (72/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696870 = | 91 (0.880) | noncoding (70/75 nt) | glnU | tRNA‑Gln | |||||