| Variant ID: vg1124043769 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24043769 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.24, others allele: 0.00, population size: 72. )
CTTCCATTTGGATTTATTGGATCTTTATTTGAATTTTAACCGAATTCAAATCGTTTCTTCGCACGTAATTTTAGAGCCCGAGGGAGTTACGGATCCAAGC[A/G]
AGGACCAAGAACCGCAAGACTTTGAGCAAGGCAAGTCATCACTATTCCTTGAACATGTTGATCCCAATTGCGAAATTGTTTTGTTTACAAATAAAATTGC
GCAATTTTATTTGTAAACAAAACAATTTCGCAATTGGGATCAACATGTTCAAGGAATAGTGATGACTTGCCTTGCTCAAAGTCTTGCGGTTCTTGGTCCT[T/C]
GCTTGGATCCGTAACTCCCTCGGGCTCTAAAATTACGTGCGAAGAAACGATTTGAATTCGGTTAAAATTCAAATAAAGATCCAATAAATCCAAATGGAAG
| 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 | 31.00% | 7.10% | 54.85% | 7.00% | NA |
| All Indica | 2759 | 12.40% | 11.70% | 73.14% | 2.75% | NA |
| All Japonica | 1512 | 58.80% | 0.40% | 24.54% | 16.27% | NA |
| Aus | 269 | 46.10% | 1.50% | 50.93% | 1.49% | NA |
| Indica I | 595 | 20.50% | 3.40% | 72.10% | 4.03% | NA |
| Indica II | 465 | 8.80% | 7.30% | 81.72% | 2.15% | NA |
| Indica III | 913 | 6.70% | 19.80% | 70.87% | 2.63% | NA |
| Indica Intermediate | 786 | 15.10% | 11.10% | 71.50% | 2.29% | NA |
| Temperate Japonica | 767 | 69.00% | 0.00% | 20.73% | 10.30% | NA |
| Tropical Japonica | 504 | 53.40% | 0.80% | 30.56% | 15.28% | NA |
| Japonica Intermediate | 241 | 37.80% | 0.80% | 24.07% | 37.34% | NA |
| VI/Aromatic | 96 | 75.00% | 0.00% | 22.92% | 2.08% | NA |
| Intermediate | 90 | 43.30% | 4.40% | 48.89% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1124043769 | A -> DEL | N | N | silent_mutation | Average:7.707; most accessible tissue: Callus, score: 15.861 | N | N | N | N |
| vg1124043769 | A -> G | LOC_Os11g40330.1 | upstream_gene_variant ; 1157.0bp to feature; MODIFIER | silent_mutation | Average:7.707; most accessible tissue: Callus, score: 15.861 | N | N | N | N |
| vg1124043769 | A -> G | LOC_Os11g40320.1 | downstream_gene_variant ; 4175.0bp to feature; MODIFIER | silent_mutation | Average:7.707; most accessible tissue: Callus, score: 15.861 | N | N | N | N |
| vg1124043769 | A -> G | LOC_Os11g40340.1 | downstream_gene_variant ; 2630.0bp to feature; MODIFIER | silent_mutation | Average:7.707; most accessible tissue: Callus, score: 15.861 | N | N | N | N |
| vg1124043769 | A -> G | LOC_Os11g40330-LOC_Os11g40340 | intergenic_region ; MODIFIER | silent_mutation | Average:7.707; most accessible tissue: Callus, score: 15.861 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124043769 | NA | 9.92E-07 | mr1517 | 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 |
| vg1124043769 | NA | 2.70E-07 | mr1538 | 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 |
| vg1124043769 | NA | 2.11E-08 | mr1517_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 |
| vg1124043769 | NA | 6.93E-11 | mr1538_2 | 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 |