| Variant ID: vg1127976659 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 27976659 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.14, others allele: 0.00, population size: 74. )
ATTGGTACAGTTCATTGAATTTTCAACTTCACATGTTAAATGTATTATTTCTATCAGGTTATTGATACGTGTATACTATTATTATATGGATGGCATTAGC[A/G]
ACGAGGCGGTTCATTAAAATTATCGAAATAGTACATTGAGCATGTGAAGTTTGAATCTTATGAGCACATATATTTTACTTGCAGGGTCTTTGTAAACAAT
ATTGTTTACAAAGACCCTGCAAGTAAAATATATGTGCTCATAAGATTCAAACTTCACATGCTCAATGTACTATTTCGATAATTTTAATGAACCGCCTCGT[T/C]
GCTAATGCCATCCATATAATAATAGTATACACGTATCAATAACCTGATAGAAATAATACATTTAACATGTGAAGTTGAAAATTCAATGAACTGTACCAAT
| 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 | 33.40% | 15.90% | 1.02% | 49.66% | NA |
| All Indica | 2759 | 29.20% | 19.80% | 0.80% | 50.24% | NA |
| All Japonica | 1512 | 38.90% | 9.90% | 1.46% | 49.74% | NA |
| Aus | 269 | 48.30% | 9.70% | 0.74% | 41.26% | NA |
| Indica I | 595 | 16.60% | 41.80% | 0.34% | 41.18% | NA |
| Indica II | 465 | 15.50% | 1.50% | 1.51% | 81.51% | NA |
| Indica III | 913 | 44.00% | 18.90% | 0.55% | 36.47% | NA |
| Indica Intermediate | 786 | 29.60% | 14.80% | 1.02% | 54.58% | NA |
| Temperate Japonica | 767 | 28.70% | 15.50% | 1.43% | 54.37% | NA |
| Tropical Japonica | 504 | 53.60% | 2.80% | 1.59% | 42.06% | NA |
| Japonica Intermediate | 241 | 40.70% | 7.10% | 1.24% | 51.04% | NA |
| VI/Aromatic | 96 | 10.40% | 24.00% | 0.00% | 65.62% | NA |
| Intermediate | 90 | 48.90% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1127976659 | A -> DEL | N | N | silent_mutation | Average:30.314; most accessible tissue: Zhenshan97 root, score: 79.962 | N | N | N | N |
| vg1127976659 | A -> G | LOC_Os11g46190.1 | upstream_gene_variant ; 1824.0bp to feature; MODIFIER | silent_mutation | Average:30.314; most accessible tissue: Zhenshan97 root, score: 79.962 | N | N | N | N |
| vg1127976659 | A -> G | LOC_Os11g46200.1 | downstream_gene_variant ; 1709.0bp to feature; MODIFIER | silent_mutation | Average:30.314; most accessible tissue: Zhenshan97 root, score: 79.962 | N | N | N | N |
| vg1127976659 | A -> G | LOC_Os11g46190-LOC_Os11g46200 | intergenic_region ; MODIFIER | silent_mutation | Average:30.314; most accessible tissue: Zhenshan97 root, score: 79.962 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1127976659 | 2.42E-06 | NA | mr1126 | 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 |
| vg1127976659 | NA | 4.10E-08 | mr1133 | 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 |
| vg1127976659 | NA | 8.10E-07 | mr1667 | 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 |
| vg1127976659 | NA | 4.96E-07 | mr1133_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 |