| Variant ID: vg0808821102 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 8821102 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAGTACATATATTTTGGTAGTTTAGTTATACAAAACCACACTATCGATGAATGTATTCACCCATGAGATATCGTGGTTGTTCCATCAAGGATGAGGACGT[T/G]
GCATCCTATTAATTTCATGCGATGGCTGGTAATAGGATGCCATGTCCTCATCCTAGGTGAAACAGTCACGTCATCTCGCGGGTGAATCCATTCATTCATA
TATGAATGAATGGATTCACCCGCGAGATGACGTGACTGTTTCACCTAGGATGAGGACATGGCATCCTATTACCAGCCATCGCATGAAATTAATAGGATGC[A/C]
ACGTCCTCATCCTTGATGGAACAACCACGATATCTCATGGGTGAATACATTCATCGATAGTGTGGTTTTGTATAACTAAACTACCAAAATATATGTACTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.00% | 16.20% | 0.57% | 8.19% | NA |
| All Indica | 2759 | 90.40% | 3.40% | 0.69% | 5.55% | NA |
| All Japonica | 1512 | 46.00% | 43.70% | 0.13% | 10.12% | NA |
| Aus | 269 | 88.80% | 0.00% | 0.00% | 11.15% | NA |
| Indica I | 595 | 79.00% | 13.60% | 0.34% | 7.06% | NA |
| Indica II | 465 | 91.40% | 0.90% | 1.08% | 6.67% | NA |
| Indica III | 913 | 96.10% | 0.10% | 0.11% | 3.72% | NA |
| Indica Intermediate | 786 | 91.90% | 0.90% | 1.40% | 5.85% | NA |
| Temperate Japonica | 767 | 21.10% | 75.00% | 0.13% | 3.78% | NA |
| Tropical Japonica | 504 | 80.20% | 5.80% | 0.20% | 13.89% | NA |
| Japonica Intermediate | 241 | 53.90% | 23.70% | 0.00% | 22.41% | NA |
| VI/Aromatic | 96 | 58.30% | 0.00% | 4.17% | 37.50% | NA |
| Intermediate | 90 | 66.70% | 14.40% | 2.22% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0808821102 | T -> G | LOC_Os08g14660.1 | upstream_gene_variant ; 4403.0bp to feature; MODIFIER | silent_mutation | Average:21.916; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0808821102 | T -> G | LOC_Os08g14670.1 | upstream_gene_variant ; 1514.0bp to feature; MODIFIER | silent_mutation | Average:21.916; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0808821102 | T -> G | LOC_Os08g14660-LOC_Os08g14670 | intergenic_region ; MODIFIER | silent_mutation | Average:21.916; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg0808821102 | T -> DEL | N | N | silent_mutation | Average:21.916; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0808821102 | 2.31E-07 | 6.79E-34 | mr1137 | 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 |
| vg0808821102 | NA | 2.89E-11 | mr1137 | 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 |
| vg0808821102 | NA | 1.56E-08 | mr1617 | 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 |
| vg0808821102 | NA | 1.22E-11 | mr1879 | 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 |
| vg0808821102 | NA | 2.30E-07 | mr1730_2 | 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 |