| Variant ID: vg0811251643 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11251643 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.03, others allele: 0.00, population size: 195. )
ACAAGTAGTCTGACTCATGGTGAGCATGCTCACAAACACCAATATCATACCCGCTAGATAAATATGTCAGACAAACTTCATCAACAATAGCCTTTTTACA[A/G]
CAAAAGGTCATAGGTTCTTCTCCGTTTGACCTCTTTTGCGGCATTTCTTCTTTCAGCATATGATTTTCTTATGCTAAAGCCTTTATCCCAAGCGTACTTG
CAAGTACGCTTGGGATAAAGGCTTTAGCATAAGAAAATCATATGCTGAAAGAAGAAATGCCGCAAAAGAGGTCAAACGGAGAAGAACCTATGACCTTTTG[T/C]
TGTAAAAAGGCTATTGTTGATGAAGTTTGTCTGACATATTTATCTAGCGGGTATGATATTGGTGTTTGTGAGCATGCTCACCATGAGTCAGACTACTTGT
| 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 | 53.90% | 9.40% | 36.50% | 0.21% | NA |
| All Indica | 2759 | 28.90% | 14.40% | 56.32% | 0.36% | NA |
| All Japonica | 1512 | 94.80% | 1.60% | 3.64% | 0.00% | NA |
| Aus | 269 | 62.80% | 5.90% | 31.23% | 0.00% | NA |
| Indica I | 595 | 16.50% | 9.60% | 73.11% | 0.84% | NA |
| Indica II | 465 | 23.20% | 14.20% | 62.58% | 0.00% | NA |
| Indica III | 913 | 40.30% | 17.60% | 41.62% | 0.44% | NA |
| Indica Intermediate | 786 | 28.40% | 14.50% | 57.00% | 0.13% | NA |
| Temperate Japonica | 767 | 95.80% | 1.70% | 2.48% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 0.60% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.00% | 3.30% | 6.64% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 5.60% | 33.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811251643 | A -> G | LOC_Os08g18860.1 | downstream_gene_variant ; 1748.0bp to feature; MODIFIER | silent_mutation | Average:14.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0811251643 | A -> G | LOC_Os08g18850.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0811251643 | A -> DEL | N | N | silent_mutation | Average:14.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |