| Variant ID: vg0137497667 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37497667 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCACCGGCATTGCCCTCCTCGTCGGAGTTGGGGGCGAACGCAAGCCGAGGGGCCGAGCCCTCGAAGCTGTCGACGATATGGTCGGCGGCATCCCGGACCT[G/A]
CGCGCGCGCGCAGTCCTCGGTCCCAGGAGGGAACTCATCCAACGCCATCCATGGAGAGAAATTGGGGTCCCTGGCCTGGTAACTCGCCAGGACGAGCTCC
GGAGCTCGTCCTGGCGAGTTACCAGGCCAGGGACCCCAATTTCTCTCCATGGATGGCGTTGGATGAGTTCCCTCCTGGGACCGAGGACTGCGCGCGCGCG[C/T]
AGGTCCGGGATGCCGCCGACCATATCGTCGACAGCTTCGAGGGCTCGGCCCCTCGGCTTGCGTTCGCCCCCAACTCCGACGAGGAGGGCAATGCCGGTGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.50% | 1.00% | 0.83% | 66.72% | NA |
| All Indica | 2759 | 2.20% | 0.00% | 0.40% | 97.39% | NA |
| All Japonica | 1512 | 84.50% | 2.80% | 1.85% | 10.85% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 1.20% | 0.00% | 0.34% | 98.49% | NA |
| Indica II | 465 | 1.50% | 0.00% | 0.22% | 98.28% | NA |
| Indica III | 913 | 0.90% | 0.00% | 0.66% | 98.47% | NA |
| Indica Intermediate | 786 | 5.00% | 0.00% | 0.25% | 94.78% | NA |
| Temperate Japonica | 767 | 84.90% | 0.00% | 2.09% | 13.04% | NA |
| Tropical Japonica | 504 | 87.70% | 8.30% | 0.60% | 3.37% | NA |
| Japonica Intermediate | 241 | 76.30% | 0.40% | 3.73% | 19.50% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 62.20% | 2.20% | 0.00% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137497667 | G -> A | LOC_Os01g64610.1 | stop_gained ; p.Gln947*; HIGH | stop_gained | Average:4.856; most accessible tissue: Callus, score: 8.749 | N | N | N | N |
| vg0137497667 | G -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:4.856; most accessible tissue: Callus, score: 8.749 | N | N | N | N |