Variant ID: vg1209159762 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 9159762 |
Reference Allele: G | Alternative Allele: A,T |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 126. )
GGGCCTCCAAGGCCCGTAGGACTCCTATTCGGATCCCTATCCGAATTAAGCTCATATTGGATCTCTATCCAATCCCCTTATTCCGGCCCATTAAGCATGC[G/A,T]
ACCCTGTAGGTTCATATATACTCGGCTGTAACCCGAAAACTCCTTTTTGGTCCACGCGTCAACAGCAGCCCCTAGCATAACGTATTGACCCACCGGGCAT
ATGCCCGGTGGGTCAATACGTTATGCTAGGGGCTGCTGTTGACGCGTGGACCAAAAAGGAGTTTTCGGGTTACAGCCGAGTATATATGAACCTACAGGGT[C/T,A]
GCATGCTTAATGGGCCGGAATAAGGGGATTGGATAGAGATCCAATATGAGCTTAATTCGGATAGGGATCCGAATAGGAGTCCTACGGGCCTTGGAGGCCC
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 | 97.20% | 2.60% | 0.28% | 0.00% | NA |
All Indica | 2759 | 96.70% | 2.80% | 0.43% | 0.00% | NA |
All Japonica | 1512 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 89.20% | 10.50% | 0.22% | 0.00% | NA |
Indica III | 913 | 98.70% | 0.10% | 1.20% | 0.00% | NA |
Indica Intermediate | 786 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 94.90% | 5.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.40% | 0.60% | 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 | 97.80% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1209159762 | G -> A | LOC_Os12g16070.1 | upstream_gene_variant ; 2376.0bp to feature; MODIFIER | silent_mutation | Average:22.684; most accessible tissue: Callus, score: 33.969 | N | N | N | N |
vg1209159762 | G -> A | LOC_Os12g16060.1 | intron_variant ; MODIFIER | silent_mutation | Average:22.684; most accessible tissue: Callus, score: 33.969 | N | N | N | N |
vg1209159762 | G -> T | LOC_Os12g16070.1 | upstream_gene_variant ; 2376.0bp to feature; MODIFIER | N | Average:22.684; most accessible tissue: Callus, score: 33.969 | N | N | N | N |
vg1209159762 | G -> T | LOC_Os12g16060.1 | intron_variant ; MODIFIER | N | Average:22.684; most accessible tissue: Callus, score: 33.969 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1209159762 | 6.78E-06 | NA | mr1912 | 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 |