| Variant ID: vg0322468242 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22468242 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 103. )
CAACTTTGGTTTTGGTGACTTTTCCATTTAAAATCATTTATTAACCCTAATTTTTCTTCGAAGTTGTCAAATTTTGAAAATTCAAAATTTGAATTGTTCA[A/G]
ATAAACTTATTTGTACAAAGGACCGATACAATAGTTGTAGATCTCGATGAGTTATACAATTTTGTTGTTTATGATTTTTGATGGTTGTGTATGTGAATGA
TCATTCACATACACAACCATCAAAAATCATAAACAACAAAATTGTATAACTCATCGAGATCTACAACTATTGTATCGGTCCTTTGTACAAATAAGTTTAT[T/C]
TGAACAATTCAAATTTTGAATTTTCAAAATTTGACAACTTCGAAGAAAAATTAGGGTTAATAAATGATTTTAAATGGAAAAGTCACCAAAACCAAAGTTG
| 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 | 50.90% | 44.70% | 4.40% | 0.00% | NA |
| All Indica | 2759 | 19.80% | 73.20% | 7.07% | 0.00% | NA |
| All Japonica | 1512 | 99.20% | 0.70% | 0.07% | 0.00% | NA |
| Aus | 269 | 77.30% | 19.70% | 2.97% | 0.00% | NA |
| Indica I | 595 | 46.90% | 46.70% | 6.39% | 0.00% | NA |
| Indica II | 465 | 8.80% | 84.90% | 6.24% | 0.00% | NA |
| Indica III | 913 | 8.90% | 84.70% | 6.46% | 0.00% | NA |
| Indica Intermediate | 786 | 18.30% | 72.90% | 8.78% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 1.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 3.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 28.90% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322468242 | A -> G | LOC_Os03g40440.1 | intron_variant ; MODIFIER | silent_mutation | Average:27.09; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0322468242 | 8.76E-06 | 7.38E-06 | mr1263_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 |
| vg0322468242 | 2.68E-06 | 1.80E-06 | mr1263_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 |