| Variant ID: vg0825763675 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 25763675 |
| Reference Allele: C | Alternative Allele: CT |
| Primary Allele: C | Secondary Allele: CT |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 309. )
GTAATCTTTGCTAGCGAAAGCTAGTGTTTTTTTTTTATGTGCACAACTCGGTGTGCCGCCATACATGCATGTGTGATCGACGTATCAGTCTGTACTCTCC[C/CT]
TTTTTTATCTTGCTAGCGAAAGCTAGTATTTTGAGTATTATTATCTGCGCAATTTGGATACCCTACATCGCTACGTGCTTTTGTAAGCTACTAACCTTGA
TCAAGGTTAGTAGCTTACAAAAGCACGTAGCGATGTAGGGTATCCAAATTGCGCAGATAATAATACTCAAAATACTAGCTTTCGCTAGCAAGATAAAAAA[G/AG]
GGAGAGTACAGACTGATACGTCGATCACACATGCATGTATGGCGGCACACCGAGTTGTGCACATAAAAAAAAAACACTAGCTTTCGCTAGCAAAGATTAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825763675 | C -> CT | LOC_Os08g40690.1 | 3_prime_UTR_variant ; 237.0bp to feature; MODIFIER | silent_mutation | Average:63.417; most accessible tissue: Callus, score: 91.712 | N | N | N | N |
| vg0825763675 | C -> CT | LOC_Os08g40680.1 | upstream_gene_variant ; 3727.0bp to feature; MODIFIER | silent_mutation | Average:63.417; most accessible tissue: Callus, score: 91.712 | N | N | N | N |
| vg0825763675 | C -> CT | LOC_Os08g40700.1 | upstream_gene_variant ; 1297.0bp to feature; MODIFIER | silent_mutation | Average:63.417; most accessible tissue: Callus, score: 91.712 | N | N | N | N |
| vg0825763675 | C -> CT | LOC_Os08g40710.1 | downstream_gene_variant ; 3873.0bp to feature; MODIFIER | silent_mutation | Average:63.417; most accessible tissue: Callus, score: 91.712 | N | N | N | N |