Variant ID: vg0912675777 (JBrowse) | Variation Type: SNP |
Chromosome: chr09 | Position: 12675777 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CACCTAAAGTTTATAGACCCAAAGTTTATAAGTCAAAAGTTTACATACCCGATTCAAATTTGAATTTGAATACAAATATTAATTTATAGACCCAAAGTTT[A/G]
TAAGTCAAAAATTTACATAACCGTTTCAATTCTGAATTTAAATTTAAATATTTATGATGTAGTAGGAAGAGAAAAAGGGAAGGAGGAAGGGGGGAGAGGA
TCCTCTCCCCCCTTCCTCCTTCCCTTTTTCTCTTCCTACTACATCATAAATATTTAAATTTAAATTCAGAATTGAAACGGTTATGTAAATTTTTGACTTA[T/C]
AAACTTTGGGTCTATAAATTAATATTTGTATTCAAATTCAAATTTGAATCGGGTATGTAAACTTTTGACTTATAAACTTTGGGTCTATAAACTTTAGGTG
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 | 96.10% | 3.80% | 0.08% | 0.00% | NA |
All Indica | 2759 | 93.80% | 6.10% | 0.14% | 0.00% | NA |
All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 90.30% | 9.10% | 0.67% | 0.00% | NA |
Indica II | 465 | 95.30% | 4.70% | 0.00% | 0.00% | NA |
Indica III | 913 | 94.50% | 5.50% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 94.70% | 5.30% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 4.40% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0912675777 | A -> G | LOC_Os09g21020.1 | upstream_gene_variant ; 1497.0bp to feature; MODIFIER | silent_mutation | Average:25.742; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
vg0912675777 | A -> G | LOC_Os09g21010.1 | downstream_gene_variant ; 3753.0bp to feature; MODIFIER | silent_mutation | Average:25.742; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
vg0912675777 | A -> G | LOC_Os09g21010-LOC_Os09g21020 | intergenic_region ; MODIFIER | silent_mutation | Average:25.742; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0912675777 | 9.95E-06 | 6.22E-06 | mr1150 | 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 |
vg0912675777 | 6.89E-07 | 7.89E-06 | mr1247_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 |