mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 27 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,334,966 | 0 | A | C | 38.0% | 147.8 / 23.4 | 113 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 3,269,981 | 0 | A | C | 37.9% | 80.7 / 10.1 | 60 | intergenic (+379/+235) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| * | NC_000913 | 2,767,445 | 0 | C | A | 37.9% | 171.9 / 20.4 | 97 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,477,265 | 0 | A | C | 34.7% | 115.4 / 30.4 | 75 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,911,533 | 0 | C | A | 34.6% | 212.2 / 21.4 | 127 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,767,444 | 0 | C | A | 34.0% | 169.0 / 14.8 | 97 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 967,676 | 0 | G | T | 31.8% | 97.4 / 11.0 | 66 | P352P (CCG→CCT) | msbA | ATP‑binding lipopolysaccharide transport protein |
| * | NC_000913 | 3,054,894 | 0 | G | T | 30.9% | 152.4 / 20.6 | 95 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 42,395 | 0 | G | T | 29.8% | 150.3 / 11.2 | 94 | intergenic (‑464/‑8) | caiT/fixA | L‑carnitine:gamma‑butyrobetaine antiporter/putative electron transfer flavoprotein FixA |
| * | NC_000913 | 2,767,449 | 0 | C | A | 29.0% | 194.5 / 17.4 | 102 | intergenic (+94/‑261) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,365,840 | 0 | T | G | 28.6% | 152.5 / 11.9 | 112 | intergenic (‑220/‑70) | ais/arnB | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| * | NC_000913 | 4,136,467 | 0 | A | C | 28.3% | 101.2 / 14.1 | 61 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 4,360,965 | 0 | C | A | 27.9% | 286.6 / 18.8 | 136 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 2,472,817 | 0 | C | A | 26.6% | 123.1 / 11.4 | 64 | G22V (GGA→GTA) | yfdN | uncharacterized protein YfdN |
| * | NC_000913 | 3,054,886 | 0 | G | T | 26.0% | 196.4 / 20.3 | 96 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 141,849 | 0 | C | A | 26.0% | 197.2 / 13.2 | 100 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| * | NC_000913 | 3,269,943 | 0 | G | T | 25.4% | 99.3 / 10.7 | 68 | intergenic (+341/+273) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| * | NC_000913 | 1,097,118 | 0 | C | A | 25.0% | 45.0 / 18.4 | 36 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,288,418 | 0 | G | T | 24.2% | 196.8 / 11.1 | 99 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 847,955 | 0 | G | A | 23.6% | 167.6 / 31.4 | 110 | 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 | = 3648146 | 121 (1.490) | 10 (0.150) | 9/482 | 4.1 | 9.6% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 91 (1.390) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 1286906 | 35 (0.430) | 8 (0.110) | 6/558 | 5.7 | 17.5% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 43 (0.570) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 4606166 | 83 (1.020) | 5 (0.090) | 3/420 | 5.9 | 7.8% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 60 (1.050) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 3469004 | 92 (1.130) | 5 (0.060) | 4/586 | 6.7 | 5.3% | coding (850/2694 nt) | chiA | endochitinase |
| ? | NC_000913 | 3469308 = | 89 (1.120) | coding (546/2694 nt) | chiA | endochitinase | |||||
| * | ? | NC_000913 | = 377391 | 57 (0.700) | 3 (0.040) | 3/572 | 7.2 | 5.6% | intergenic (+80/+144) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | 377492 = | 46 (0.590) | intergenic (+181/+43) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 2357665 | 92 (1.130) | 3 (0.040) | 3/594 | 7.3 | 3.3% | coding (762/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357848 = | 86 (1.060) | intergenic (+45/+194) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||