| Variant ID: vg0321868645 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21868645 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.28, others allele: 0.00, population size: 100. )
GTTTTTGCCGCCTCAACATGCGGTTGATCCAGTACCGCAGCAGCCGATTCAGCAGACACCCCCAATTCAGCAGGTTATGCAACCAATCCAGCAACAGGTC[G/A]
TGTAACCAGTTCAGCAAACATCACCAAGGCAGCAGCCTCTGCAACCGATCCAACAGACTACGTTAAGGCAGCAAATCATTCAGCCGATTCAGCAACAGGG
CCCTGTTGCTGAATCGGCTGAATGATTTGCTGCCTTAACGTAGTCTGTTGGATCGGTTGCAGAGGCTGCTGCCTTGGTGATGTTTGCTGAACTGGTTACA[C/T]
GACCTGTTGCTGGATTGGTTGCATAACCTGCTGAATTGGGGGTGTCTGCTGAATCGGCTGCTGCGGTACTGGATCAACCGCATGTTGAGGCGGCAAAAAC
| 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 | 61.60% | 4.50% | 1.23% | 32.67% | NA |
| All Indica | 2759 | 48.00% | 4.00% | 1.78% | 46.21% | NA |
| All Japonica | 1512 | 98.10% | 0.20% | 0.00% | 1.65% | NA |
| Aus | 269 | 14.10% | 0.40% | 2.60% | 82.90% | NA |
| Indica I | 595 | 84.70% | 4.00% | 1.85% | 9.41% | NA |
| Indica II | 465 | 39.80% | 3.90% | 1.94% | 54.41% | NA |
| Indica III | 913 | 31.80% | 1.20% | 0.99% | 66.05% | NA |
| Indica Intermediate | 786 | 44.00% | 7.30% | 2.54% | 46.18% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 0.00% | 4.76% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 4.20% | 92.70% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 67.80% | 10.00% | 2.22% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321868645 | G -> A | LOC_Os03g39350.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.219; most accessible tissue: Minghui63 flag leaf, score: 81.811 | N | N | N | N |
| vg0321868645 | G -> DEL | N | N | silent_mutation | Average:68.219; most accessible tissue: Minghui63 flag leaf, score: 81.811 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0321868645 | NA | 4.23E-08 | mr1169_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 |
| vg0321868645 | 1.10E-06 | 1.10E-06 | mr1666_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 |
| vg0321868645 | NA | 6.46E-06 | mr1851_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 |