| Variant ID: vg0332500781 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 32500781 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 120. )
TATTGCAAAAAAGCATGTTCTATCACCACAATTTTAATTTTTGTGGCAATTTATATAGTACATGGTACTTTTCACTATTTTTTGTTGCCACGATCAACAA[A/G]
TTCGTTGCAATAAAAAAATTGTTGTCTCATAATTTAACTTATTTTTTTCATATGGACTCGGATTGAGACAAATTTTATATGGAAATTATAGCTCTCGACG
CGTCGAGAGCTATAATTTCCATATAAAATTTGTCTCAATCCGAGTCCATATGAAAAAAATAAGTTAAATTATGAGACAACAATTTTTTTATTGCAACGAA[T/C]
TTGTTGATCGTGGCAACAAAAAATAGTGAAAAGTACCATGTACTATATAAATTGCCACAAAAATTAAAATTGTGGTGATAGAACATGCTTTTTTGCAATA
| 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 | 92.00% | 2.00% | 3.34% | 2.67% | NA |
| All Indica | 2759 | 86.70% | 3.20% | 5.55% | 4.49% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.80% | 1.80% | 5.88% | 1.51% | NA |
| Indica II | 465 | 88.80% | 3.20% | 3.01% | 4.95% | NA |
| Indica III | 913 | 86.30% | 2.80% | 3.50% | 7.34% | NA |
| Indica Intermediate | 786 | 83.00% | 4.70% | 9.16% | 3.18% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 3.30% | 4.44% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0332500781 | A -> DEL | N | N | silent_mutation | Average:20.162; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0332500781 | A -> G | LOC_Os03g57020-LOC_Os03g57030 | intergenic_region ; MODIFIER | silent_mutation | Average:20.162; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0332500781 | 6.82E-07 | NA | mr1723 | 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 |
| vg0332500781 | 3.55E-07 | 8.90E-09 | mr1723 | 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 |
| vg0332500781 | NA | 8.05E-06 | mr1734 | 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 |
| vg0332500781 | 5.57E-09 | NA | mr1723_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 |
| vg0332500781 | 8.73E-09 | 5.50E-13 | mr1723_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 |