| Variant ID: vg0521976037 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21976037 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.12, others allele: 0.00, population size: 49. )
TGCTATCTTCTAGGAAAGTTCAGTATGTATCACATAGAAAAGTTCAGTGTGTGCTATATTGCAGAGGAGTTCAGTATGTTGCACAGAAAATTCAGAACAT[A/G]
CTATATGCTGTCGTATAACAAAGTTCAGTACATAGCCTCCCATAGAAAAATTCAGTATATATGTGAAAAATTCAGTAAATACTAGTGCGTATCAAAGTTC
GAACTTTGATACGCACTAGTATTTACTGAATTTTTCACATATATACTGAATTTTTCTATGGGAGGCTATGTACTGAACTTTGTTATACGACAGCATATAG[T/C]
ATGTTCTGAATTTTCTGTGCAACATACTGAACTCCTCTGCAATATAGCACACACTGAACTTTTCTATGTGATACATACTGAACTTTCCTAGAAGATAGCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.60% | 3.50% | 13.82% | 44.12% | NA |
| All Indica | 2759 | 2.50% | 5.90% | 21.46% | 70.13% | NA |
| All Japonica | 1512 | 98.70% | 0.00% | 0.40% | 0.93% | NA |
| Aus | 269 | 45.40% | 0.00% | 16.36% | 38.29% | NA |
| Indica I | 595 | 1.30% | 9.60% | 17.14% | 71.93% | NA |
| Indica II | 465 | 2.60% | 1.10% | 12.04% | 84.30% | NA |
| Indica III | 913 | 0.90% | 7.00% | 31.43% | 60.68% | NA |
| Indica Intermediate | 786 | 5.30% | 4.60% | 18.70% | 71.37% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.26% | 1.04% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 1.24% | 1.24% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 48.90% | 4.40% | 12.22% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521976037 | A -> DEL | N | N | silent_mutation | Average:10.26; most accessible tissue: Callus, score: 24.036 | N | N | N | N |
| vg0521976037 | A -> G | LOC_Os05g37530.1 | downstream_gene_variant ; 4854.0bp to feature; MODIFIER | silent_mutation | Average:10.26; most accessible tissue: Callus, score: 24.036 | N | N | N | N |
| vg0521976037 | A -> G | LOC_Os05g37550.1 | downstream_gene_variant ; 4050.0bp to feature; MODIFIER | silent_mutation | Average:10.26; most accessible tissue: Callus, score: 24.036 | N | N | N | N |
| vg0521976037 | A -> G | LOC_Os05g37540.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.26; most accessible tissue: Callus, score: 24.036 | N | N | N | N |