| Variant ID: vg0820000626 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 20000626 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGTCACAGATAACCTCATCTCAATCGGGCATTTAGTTATGGCCCGTCACAGATGACTATAATCCACAAAAAAAATAAATTTTGTTTTTTTGGCTAGCCT[C/T]
AGGCCTTTGCTAGCCATGCCCGCTGCAAAAATGACAGAAACAAACACAGATATCAAATATCCCCAGCTCTCCAGCATCACCCATTCATACATATGCATTC
GAATGCATATGTATGAATGGGTGATGCTGGAGAGCTGGGGATATTTGATATCTGTGTTTGTTTCTGTCATTTTTGCAGCGGGCATGGCTAGCAAAGGCCT[G/A]
AGGCTAGCCAAAAAAACAAAATTTATTTTTTTTGTGGATTATAGTCATCTGTGACGGGCCATAACTAAATGCCCGATTGAGATGAGGTTATCTGTGACGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.80% | 0.80% | 1.99% | 9.44% | NA |
| All Indica | 2759 | 79.90% | 1.40% | 3.26% | 15.44% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.07% | 0.13% | NA |
| Aus | 269 | 98.10% | 0.00% | 0.00% | 1.86% | NA |
| Indica I | 595 | 97.00% | 0.30% | 0.17% | 2.52% | NA |
| Indica II | 465 | 86.70% | 0.90% | 4.09% | 8.39% | NA |
| Indica III | 913 | 66.60% | 2.40% | 4.82% | 26.18% | NA |
| Indica Intermediate | 786 | 78.50% | 1.30% | 3.31% | 16.92% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 3.12% | 7.29% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0820000626 | C -> T | LOC_Os08g32280.1 | downstream_gene_variant ; 396.0bp to feature; MODIFIER | silent_mutation | Average:22.362; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
| vg0820000626 | C -> T | LOC_Os08g32270-LOC_Os08g32280 | intergenic_region ; MODIFIER | silent_mutation | Average:22.362; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
| vg0820000626 | C -> DEL | N | N | silent_mutation | Average:22.362; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0820000626 | NA | 3.69E-07 | mr1411 | Ind_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 |
| vg0820000626 | NA | 2.35E-06 | mr1403_2 | Ind_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 |
| vg0820000626 | NA | 6.11E-06 | mr1482_2 | Ind_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 |
| vg0820000626 | 2.85E-06 | 2.84E-06 | mr1487_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 |