| Variant ID: vg0710993311 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10993311 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )
TCGTTTCCTGAAGAAAACCAAGACGTACAGCATGTCAAGATGTCCATGTCCAAATTCACAACATATACTGATATATACGTGTGTCAAATCAAATCGAAGG[C/A]
TCATGAACTCAGGGAGGTTTCAGCTGCTATGCTACGTACCTGAATAATTACAGTTCCAAGATCAAGTTTGGTGATTTTGTCGGACAGGTAGCCCAATACC
GGTATTGGGCTACCTGTCCGACAAAATCACCAAACTTGATCTTGGAACTGTAATTATTCAGGTACGTAGCATAGCAGCTGAAACCTCCCTGAGTTCATGA[G/T]
CCTTCGATTTGATTTGACACACGTATATATCAGTATATGTTGTGAATTTGGACATGGACATCTTGACATGCTGTACGTCTTGGTTTTCTTCAGGAAACGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 95.50% | 4.50% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 87.10% | 12.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0710993311 | C -> A | LOC_Os07g18580.1 | upstream_gene_variant ; 3779.0bp to feature; MODIFIER | silent_mutation | Average:64.299; most accessible tissue: Callus, score: 88.323 | N | N | N | N |
| vg0710993311 | C -> A | LOC_Os07g18610.1 | upstream_gene_variant ; 4732.0bp to feature; MODIFIER | silent_mutation | Average:64.299; most accessible tissue: Callus, score: 88.323 | N | N | N | N |
| vg0710993311 | C -> A | LOC_Os07g18590.1 | downstream_gene_variant ; 870.0bp to feature; MODIFIER | silent_mutation | Average:64.299; most accessible tissue: Callus, score: 88.323 | N | N | N | N |
| vg0710993311 | C -> A | LOC_Os07g18600.1 | intron_variant ; MODIFIER | silent_mutation | Average:64.299; most accessible tissue: Callus, score: 88.323 | N | N | N | N |