| Variant ID: vg0207033058 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 7033058 |
| Reference Allele: A | Alternative Allele: AC |
| Primary Allele: A | Secondary Allele: AC |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 345. )
GTCATAGAGTTTTGCAGGAAAGAAATATTATGCCAACTTGCCAAGCCAACACAATATGATGCCAAAGATGGTGCAAGAGGACAAGAGAAATAGTGGATGC[A/AC]
CCATGTAGTGTGTTTCTTGCGGACTTACCATTACAGGACTGTTGTTGAACAGAGCTCTGAAAGCAACAAATCCAACCAAATAACCCGTGAACATTATAAG
CTTATAATGTTCACGGGTTATTTGGTTGGATTTGTTGCTTTCAGAGCTCTGTTCAACAACAGTCCTGTAATGGTAAGTCCGCAAGAAACACACTACATGG[T/GT]
GCATCCACTATTTCTCTTGTCCTCTTGCACCATCTTTGGCATCATATTGTGTTGGCTTGGCAAGTTGGCATAATATTTCTTTCCTGCAAAACTCTATGAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 69.50% | 30.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 87.40% | 12.60% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.40% | 3.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0207033058 | A -> AC | LOC_Os02g13190.1 | upstream_gene_variant ; 4755.0bp to feature; MODIFIER | silent_mutation | Average:71.147; most accessible tissue: Callus, score: 85.843 | N | N | N | N |
| vg0207033058 | A -> AC | LOC_Os02g13200.1 | intron_variant ; MODIFIER | silent_mutation | Average:71.147; most accessible tissue: Callus, score: 85.843 | N | N | N | N |