| Variant ID: vg0110539868 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 10539868 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, G: 0.08, others allele: 0.00, population size: 97. )
GTGCGGGACCGCCTCAGGGGTCTGCGAAACCAGGGCCTAACGGGGGCGATGGTTTTTGGTGACTACTTCCATTGCCGCATCGCACCCCTCCAGGAGCGGT[C/G]
CCGTGGCGCATGGGAGTACACTGGGCCCAACGATCCCATGCGCACCCATGTGGGTGAGCGCTGGGACTAGGGCGAGGAGGGCGCGAAGATGGTGATCTGG
CCAGATCACCATCTTCGCGCCCTCCTCGCCCTAGTCCCAGCGCTCACCCACATGGGTGCGCATGGGATCGTTGGGCCCAGTGTACTCCCATGCGCCACGG[G/C]
ACCGCTCCTGGAGGGGTGCGATGCGGCAATGGAAGTAGTCACCAAAAACCATCGCCCCCGTTAGGCCCTGGTTTCGCAGACCCCTGAGGCGGTCCCGCAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.20% | 33.10% | 0.72% | 32.95% | NA |
| All Indica | 2759 | 1.50% | 49.40% | 1.05% | 48.06% | NA |
| All Japonica | 1512 | 96.70% | 2.40% | 0.07% | 0.79% | NA |
| Aus | 269 | 1.10% | 28.30% | 1.12% | 69.52% | NA |
| Indica I | 595 | 2.00% | 18.30% | 1.85% | 77.82% | NA |
| Indica II | 465 | 1.30% | 38.30% | 1.29% | 59.14% | NA |
| Indica III | 913 | 1.10% | 75.10% | 0.44% | 23.33% | NA |
| Indica Intermediate | 786 | 1.70% | 49.60% | 1.02% | 47.71% | NA |
| Temperate Japonica | 767 | 98.20% | 0.80% | 0.13% | 0.91% | NA |
| Tropical Japonica | 504 | 94.80% | 4.60% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 95.90% | 3.30% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 22.90% | 72.90% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 47.80% | 20.00% | 1.11% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0110539868 | C -> G | LOC_Os01g18680.1 | upstream_gene_variant ; 196.0bp to feature; MODIFIER | silent_mutation | Average:12.432; most accessible tissue: Callus, score: 29.956 | N | N | N | N |
| vg0110539868 | C -> G | LOC_Os01g18690.1 | downstream_gene_variant ; 1942.0bp to feature; MODIFIER | silent_mutation | Average:12.432; most accessible tissue: Callus, score: 29.956 | N | N | N | N |
| vg0110539868 | C -> G | LOC_Os01g18670-LOC_Os01g18680 | intergenic_region ; MODIFIER | silent_mutation | Average:12.432; most accessible tissue: Callus, score: 29.956 | N | N | N | N |
| vg0110539868 | C -> DEL | N | N | silent_mutation | Average:12.432; most accessible tissue: Callus, score: 29.956 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0110539868 | NA | 7.48E-07 | mr1690 | 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 |
| vg0110539868 | NA | 7.28E-24 | mr1888 | 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 |
| vg0110539868 | NA | 1.81E-13 | mr1216_2 | 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 |
| vg0110539868 | NA | 1.33E-16 | mr1416_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 |
| vg0110539868 | NA | 8.38E-46 | mr1519_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 |