| Variant ID: vg0403660277 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3660277 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 81. )
CCCAATCGATACCTATACTTTTCAACGAATCAAAAAAAAAAATCCCGCCTACCATCGCCGCCACTTTGCCACCTTATCCACCACCACCGCCGCCGTGGCC[G/A]
CCACCATCTCGCATGCCACGGTTGCTGCCCAATCCGCCATTAATTCCAATCGGCATCAGCTAGGCTACATACGTACGTGGTTAACGCAGTCCGATCTGTT
AACAGATCGGACTGCGTTAACCACGTACGTATGTAGCCTAGCTGATGCCGATTGGAATTAATGGCGGATTGGGCAGCAACCGTGGCATGCGAGATGGTGG[C/T]
GGCCACGGCGGCGGTGGTGGTGGATAAGGTGGCAAAGTGGCGGCGATGGTAGGCGGGATTTTTTTTTTTGATTCGTTGAAAAGTATAGGTATCGATTGGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.90% | 27.10% | 0.93% | 13.01% | NA |
| All Indica | 2759 | 48.20% | 44.40% | 0.76% | 6.60% | NA |
| All Japonica | 1512 | 76.30% | 2.00% | 0.79% | 20.90% | NA |
| Aus | 269 | 55.80% | 0.00% | 2.97% | 41.26% | NA |
| Indica I | 595 | 7.20% | 90.90% | 0.17% | 1.68% | NA |
| Indica II | 465 | 39.40% | 48.40% | 1.08% | 11.18% | NA |
| Indica III | 913 | 76.00% | 17.70% | 0.88% | 5.37% | NA |
| Indica Intermediate | 786 | 52.30% | 37.80% | 0.89% | 9.03% | NA |
| Temperate Japonica | 767 | 63.40% | 0.80% | 0.91% | 34.94% | NA |
| Tropical Japonica | 504 | 92.90% | 4.00% | 0.20% | 2.98% | NA |
| Japonica Intermediate | 241 | 83.00% | 1.70% | 1.66% | 13.69% | NA |
| VI/Aromatic | 96 | 95.80% | 2.10% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 63.30% | 28.90% | 2.22% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403660277 | G -> DEL | N | N | silent_mutation | Average:46.801; most accessible tissue: Callus, score: 76.926 | N | N | N | N |
| vg0403660277 | G -> A | LOC_Os04g06920.1 | upstream_gene_variant ; 2373.0bp to feature; MODIFIER | silent_mutation | Average:46.801; most accessible tissue: Callus, score: 76.926 | N | N | N | N |
| vg0403660277 | G -> A | LOC_Os04g06940.1 | downstream_gene_variant ; 2621.0bp to feature; MODIFIER | silent_mutation | Average:46.801; most accessible tissue: Callus, score: 76.926 | N | N | N | N |
| vg0403660277 | G -> A | LOC_Os04g06920-LOC_Os04g06940 | intergenic_region ; MODIFIER | silent_mutation | Average:46.801; most accessible tissue: Callus, score: 76.926 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403660277 | NA | 2.48E-06 | mr1037 | 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 |
| vg0403660277 | NA | 8.54E-08 | mr1037_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 |
| vg0403660277 | 1.25E-09 | NA | mr1798_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 |
| vg0403660277 | 5.46E-10 | 4.25E-13 | mr1798_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 |