| Variant ID: vg0517742966 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 17742966 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 74. )
CATCATGGCCGCCGATCAGATCCTCGCGCAGCCTTGGTGGGTTGGCTCACGAACATGGCGGTTTGGCCTAGCTGAGACGATGGTGCTGCTATTTCCACTG[C/T]
CAACATCGTCGGCTGATGGAAAAGAGAGGAGAGAGGAAGATAGTGAGGGGAAAAGAGGAGAGTCATTGATATATAGGACCCACATTTTATGTTAGCAAAC
GTTTGCTAACATAAAATGTGGGTCCTATATATCAATGACTCTCCTCTTTTCCCCTCACTATCTTCCTCTCTCCTCTCTTTTCCATCAGCCGACGATGTTG[G/A]
CAGTGGAAATAGCAGCACCATCGTCTCAGCTAGGCCAAACCGCCATGTTCGTGAGCCAACCCACCAAGGCTGCGCGAGGATCTGATCGGCGGCCATGATG
| 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 | 38.00% | 15.70% | 2.22% | 44.05% | NA |
| All Indica | 2759 | 10.00% | 23.30% | 3.37% | 63.36% | NA |
| All Japonica | 1512 | 91.30% | 2.40% | 0.07% | 6.28% | NA |
| Aus | 269 | 3.70% | 19.30% | 3.35% | 73.61% | NA |
| Indica I | 595 | 8.10% | 32.30% | 5.71% | 53.95% | NA |
| Indica II | 465 | 31.40% | 17.00% | 2.80% | 48.82% | NA |
| Indica III | 913 | 2.10% | 18.90% | 1.64% | 77.33% | NA |
| Indica Intermediate | 786 | 8.00% | 25.20% | 3.94% | 62.85% | NA |
| Temperate Japonica | 767 | 97.30% | 0.50% | 0.00% | 2.22% | NA |
| Tropical Japonica | 504 | 79.20% | 5.80% | 0.20% | 14.88% | NA |
| Japonica Intermediate | 241 | 97.50% | 1.20% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 88.50% | 5.20% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 52.20% | 6.70% | 2.22% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0517742966 | C -> T | LOC_Os05g30630.1 | upstream_gene_variant ; 135.0bp to feature; MODIFIER | silent_mutation | Average:64.532; most accessible tissue: Callus, score: 95.885 | N | N | N | N |
| vg0517742966 | C -> T | LOC_Os05g30620.1 | downstream_gene_variant ; 4448.0bp to feature; MODIFIER | silent_mutation | Average:64.532; most accessible tissue: Callus, score: 95.885 | N | N | N | N |
| vg0517742966 | C -> T | LOC_Os05g30630-LOC_Os05g30640 | intergenic_region ; MODIFIER | silent_mutation | Average:64.532; most accessible tissue: Callus, score: 95.885 | N | N | N | N |
| vg0517742966 | C -> DEL | N | N | silent_mutation | Average:64.532; most accessible tissue: Callus, score: 95.885 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0517742966 | 6.63E-07 | 6.63E-07 | mr1827 | 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 |
| vg0517742966 | NA | 1.30E-08 | mr1399_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 |
| vg0517742966 | 4.40E-07 | 1.09E-08 | mr1399_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 |
| vg0517742966 | NA | 7.15E-06 | mr1827_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 |