| Variant ID: vg0715383438 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 15383438 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.07, others allele: 0.00, population size: 107. )
CGATCGACGTAGGCAACGCAGTTGCGCTTGTACTGCTCGATGATGTTGCACTACTAGAAAAATAGTTTTTCGAGGCAGCCAAAAATGGTTTTTCAGGCGG[G/A]
GGAAAGGACCGCCTGCATGCAAAGACTTGCGAAAATAGATGGGTCCACCATTGAAAATCATTTTTGCAGGCGGCATCTATTTTTATAGGCGGTAGAACCA
TGGTTCTACCGCCTATAAAAATAGATGCCGCCTGCAAAAATGATTTTCAATGGTGGACCCATCTATTTTCGCAAGTCTTTGCATGCAGGCGGTCCTTTCC[C/T]
CCGCCTGAAAAACCATTTTTGGCTGCCTCGAAAAACTATTTTTCTAGTAGTGCAACATCATCGAGCAGTACAAGCGCAACTGCGTTGCCTACGTCGATCG
| 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 | 77.90% | 22.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 70.30% | 29.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 23.40% | 76.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 60.50% | 39.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.20% | 8.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 69.00% | 31.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 66.80% | 33.20% | 0.00% | 0.00% | 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 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 13.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715383438 | G -> A | LOC_Os07g26670.1 | downstream_gene_variant ; 2438.0bp to feature; MODIFIER | silent_mutation | Average:75.706; most accessible tissue: Callus, score: 88.1 | N | N | N | N |
| vg0715383438 | G -> A | LOC_Os07g26660-LOC_Os07g26670 | intergenic_region ; MODIFIER | silent_mutation | Average:75.706; most accessible tissue: Callus, score: 88.1 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715383438 | NA | 3.26E-06 | mr1028 | 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 |
| vg0715383438 | NA | 8.29E-06 | mr1397 | 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 |
| vg0715383438 | NA | 3.62E-08 | mr1857 | 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 |