| Variant ID: vg0329917563 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29917563 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 96. )
TATGACTTTGAAATGTGCTAAAAAATTTTGCACTGCTATATATGTGCCCCCCTAGTTTTACAATGTCAAAAGCATTGATAAAATTATATAACAACTAAGG[A/G]
CGATATAACAATATCGGCCATTGTACATCGGCAAACCACAACCGAGTACACCATGAAAAACAACTAAGGGCGATATAACCATATCGGCCATCTCTAGGCG
CGCCTAGAGATGGCCGATATGGTTATATCGCCCTTAGTTGTTTTTCATGGTGTACTCGGTTGTGGTTTGCCGATGTACAATGGCCGATATTGTTATATCG[T/C]
CCTTAGTTGTTATATAATTTTATCAATGCTTTTGACATTGTAAAACTAGGGGGGCACATATATAGCAGTGCAAAATTTTTTAGCACATTTCAAAGTCATA
| 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 | 37.20% | 15.10% | 7.41% | 40.29% | NA |
| All Indica | 2759 | 4.60% | 25.00% | 10.62% | 59.77% | NA |
| All Japonica | 1512 | 98.80% | 0.70% | 0.07% | 0.46% | NA |
| Aus | 269 | 2.20% | 0.70% | 17.10% | 79.93% | NA |
| Indica I | 595 | 5.90% | 30.10% | 7.56% | 56.47% | NA |
| Indica II | 465 | 4.50% | 31.80% | 12.47% | 51.18% | NA |
| Indica III | 913 | 2.20% | 20.80% | 11.94% | 65.06% | NA |
| Indica Intermediate | 786 | 6.50% | 22.00% | 10.31% | 61.20% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 97.80% | 1.60% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 88.50% | 1.00% | 3.12% | 7.29% | NA |
| Intermediate | 90 | 51.10% | 12.20% | 7.78% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329917563 | A -> DEL | N | N | silent_mutation | Average:5.329; most accessible tissue: Callus, score: 9.083 | N | N | N | N |
| vg0329917563 | A -> G | LOC_Os03g52100.1 | downstream_gene_variant ; 246.0bp to feature; MODIFIER | silent_mutation | Average:5.329; most accessible tissue: Callus, score: 9.083 | N | N | N | N |
| vg0329917563 | A -> G | LOC_Os03g52110.1 | downstream_gene_variant ; 1091.0bp to feature; MODIFIER | silent_mutation | Average:5.329; most accessible tissue: Callus, score: 9.083 | N | N | N | N |
| vg0329917563 | A -> G | LOC_Os03g52100-LOC_Os03g52110 | intergenic_region ; MODIFIER | silent_mutation | Average:5.329; most accessible tissue: Callus, score: 9.083 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0329917563 | 1.22E-06 | NA | mr1297 | 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 |
| vg0329917563 | 2.19E-06 | 4.58E-06 | mr1434 | 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 |
| vg0329917563 | 4.28E-06 | 4.28E-06 | mr1628 | 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 |
| vg0329917563 | 1.06E-06 | 1.06E-06 | mr1784 | 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 |