| Variant ID: vg0811907223 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11907223 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAATAATATCCATGTCATTTTATAGCCAATATCAAAACTAACTAGTACAATAGGTTGGCTATTATATCAACATGATCTCATTATTCAAACAATAAACTTT[A/G]
CATGTGCATGATCAGAAACGCCCTCAACTCTGTGGCCTATATGGCCATTTGTATTATGCAATAAACATGGGTTATCTACTACTCTACCTGAAAAAATAAC
GTTATTTTTTCAGGTAGAGTAGTAGATAACCCATGTTTATTGCATAATACAAATGGCCATATAGGCCACAGAGTTGAGGGCGTTTCTGATCATGCACATG[T/C]
AAAGTTTATTGTTTGAATAATGAGATCATGTTGATATAATAGCCAACCTATTGTACTAGTTAGTTTTGATATTGGCTATAAAATGACATGGATATTATTG
| 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 | 91.80% | 0.70% | 4.82% | 2.69% | NA |
| All Indica | 2759 | 91.80% | 0.90% | 7.10% | 0.22% | NA |
| All Japonica | 1512 | 90.30% | 0.40% | 1.52% | 7.80% | NA |
| Aus | 269 | 98.90% | 0.40% | 0.74% | 0.00% | NA |
| Indica I | 595 | 98.30% | 0.00% | 1.68% | 0.00% | NA |
| Indica II | 465 | 95.50% | 0.40% | 3.87% | 0.22% | NA |
| Indica III | 913 | 85.50% | 2.40% | 11.50% | 0.55% | NA |
| Indica Intermediate | 786 | 92.00% | 0.00% | 8.02% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 74.20% | 1.20% | 4.17% | 20.44% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 0.83% | 5.39% | NA |
| VI/Aromatic | 96 | 92.70% | 1.00% | 5.21% | 1.04% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 2.22% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811907223 | A -> G | LOC_Os08g19870.1 | upstream_gene_variant ; 431.0bp to feature; MODIFIER | silent_mutation | Average:57.65; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg0811907223 | A -> G | LOC_Os08g19880.1 | upstream_gene_variant ; 2573.0bp to feature; MODIFIER | silent_mutation | Average:57.65; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg0811907223 | A -> G | LOC_Os08g19860.1 | downstream_gene_variant ; 3647.0bp to feature; MODIFIER | silent_mutation | Average:57.65; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg0811907223 | A -> G | LOC_Os08g19890.1 | downstream_gene_variant ; 4270.0bp to feature; MODIFIER | silent_mutation | Average:57.65; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg0811907223 | A -> G | LOC_Os08g19870-LOC_Os08g19880 | intergenic_region ; MODIFIER | silent_mutation | Average:57.65; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| vg0811907223 | A -> DEL | N | N | silent_mutation | Average:57.65; most accessible tissue: Zhenshan97 root, score: 75.661 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0811907223 | 1.09E-06 | 1.86E-08 | mr1682 | Jap_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 |
| vg0811907223 | NA | 8.41E-07 | mr1695 | Jap_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 |
| vg0811907223 | NA | 6.34E-06 | mr1817 | Jap_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 |