| Variant ID: vg0800728758 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 728758 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TTTTTTGTAAAAATTTTCTATAGGAAAGTTGCTTTAAAAAACCATATTAATCCATTTTTAAAATTTAAAATAATTAATACTCAATTAATCATGAGCTAAT[A/G]
GCTCACCTCATTTTACGTATCTTCTCAATCTTCTCAATCCCCTTCTTCTCAAACACACCCTCACTCTCTTTTACTGTTTTTCTCTCGCTTCTTTACCTTT
AAAGGTAAAGAAGCGAGAGAAAAACAGTAAAAGAGAGTGAGGGTGTGTTTGAGAAGAAGGGGATTGAGAAGATTGAGAAGATACGTAAAATGAGGTGAGC[T/C]
ATTAGCTCATGATTAATTGAGTATTAATTATTTTAAATTTTAAAAATGGATTAATATGGTTTTTTAAAGCAACTTTCCTATAGAAAATTTTTACAAAAAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.80% | 39.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 90.60% | 9.30% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 3.70% | 96.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.90% | 8.90% | 0.17% | 0.00% | NA |
| Indica II | 465 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 88.70% | 11.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 88.50% | 11.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 1.60% | 98.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 7.70% | 92.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 5.20% | 94.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 51.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0800728758 | A -> G | LOC_Os08g02160.1 | upstream_gene_variant ; 3265.0bp to feature; MODIFIER | silent_mutation | Average:44.221; most accessible tissue: Callus, score: 60.707 | N | N | N | N |
| vg0800728758 | A -> G | LOC_Os08g02150-LOC_Os08g02160 | intergenic_region ; MODIFIER | silent_mutation | Average:44.221; most accessible tissue: Callus, score: 60.707 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0800728758 | NA | 2.21E-07 | mr1659 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0800728758 | NA | 6.44E-07 | mr1785 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0800728758 | NA | 4.55E-11 | mr1216_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0800728758 | NA | 3.00E-06 | mr1836_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |