| Variant ID: vg0704005849 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4005849 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 134. )
TTTTTAACTCCTCTTTGGAAGGGTTTTGGAGGTACGAGATAATCTTGTTAATTTAACTAGTGTGGAAAGGCTCAATCTTGATCTGATTAACGTATATGGC[A/G]
CTGTTGATCGATCATTGGACCCAGCTTTTCAGAAAGGAGAGATAGAGAGATCTTGGGTATGTTCATATATGTCTCCAGCTCTCTGGAGGTCGTTGGAGCT
AGCTCCAACGACCTCCAGAGAGCTGGAGACATATATGAACATACCCAAGATCTCTCTATCTCTCCTTTCTGAAAAGCTGGGTCCAATGATCGATCAACAG[T/C]
GCCATATACGTTAATCAGATCAAGATTGAGCCTTTCCACACTAGTTAAATTAACAAGATTATCTCGTACCTCCAAAACCCTTCCAAAGAGGAGTTAAAAA
| 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 | 95.90% | 3.10% | 1.02% | 0.00% | NA |
| All Indica | 2759 | 93.30% | 5.30% | 1.41% | 0.00% | NA |
| All Japonica | 1512 | 99.40% | 0.00% | 0.60% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.50% | 0.00% | 1.51% | 0.00% | NA |
| Indica II | 465 | 82.40% | 13.50% | 4.09% | 0.00% | NA |
| Indica III | 913 | 98.00% | 1.60% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 90.20% | 8.80% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 99.10% | 0.00% | 0.91% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0704005849 | A -> G | LOC_Os07g07960.1 | upstream_gene_variant ; 870.0bp to feature; MODIFIER | silent_mutation | Average:69.056; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |
| vg0704005849 | A -> G | LOC_Os07g07960-LOC_Os07g07974 | intergenic_region ; MODIFIER | silent_mutation | Average:69.056; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0704005849 | NA | 2.46E-06 | mr1598 | 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 |
| vg0704005849 | 3.81E-07 | NA | mr1319_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 |
| vg0704005849 | 1.67E-06 | NA | mr1319_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 |