| Variant ID: vg0630422972 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 30422972 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 322. )
TGGCGGCTCAAGCGATAGTCCTCCCTTGCTACCTTGGTCTTGCGAACCCGACATTTGTACTTCTTGTAATAATACATCTGCATAATTGTAAACTCTAAGC[A/C]
CAAAAACATGAAAGCTCTAGCTGTTTAATCTATGCATCACACGAAAAATACTACCTAACAGTATCTAACGCATCAAAAGCCACACATTTACCAAAAGAAT
ATTCTTTTGGTAAATGTGTGGCTTTTGATGCGTTAGATACTGTTAGGTAGTATTTTTCGTGTGATGCATAGATTAAACAGCTAGAGCTTTCATGTTTTTG[T/G]
GCTTAGAGTTTACAATTATGCAGATGTATTATTACAAGAAGTACAAATGTCGGGTTCGCAAGACCAAGGTAGCAAGGGAGGACTATCGCTTGAGCCGCCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0630422972 | A -> C | LOC_Os06g50240.1 | 3_prime_UTR_variant ; 616.0bp to feature; MODIFIER | N | Average:54.719; most accessible tissue: Callus, score: 81.891 | N | N | N | N |
| vg0630422972 | A -> C | LOC_Os06g50260.1 | upstream_gene_variant ; 1994.0bp to feature; MODIFIER | N | Average:54.719; most accessible tissue: Callus, score: 81.891 | N | N | N | N |
| vg0630422972 | A -> C | LOC_Os06g50230.1 | downstream_gene_variant ; 4127.0bp to feature; MODIFIER | N | Average:54.719; most accessible tissue: Callus, score: 81.891 | N | N | N | N |
| vg0630422972 | A -> C | LOC_Os06g50250.1 | intron_variant ; MODIFIER | N | Average:54.719; most accessible tissue: Callus, score: 81.891 | N | N | N | N |