Variant ID: vg0222037003 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 22037003 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.57, G: 0.42, others allele: 0.00, population size: 99. )
AAATACGTTTAAAATAGAGTCAACAAATATTTCAAAAATATGATCCACACATAAACATTCGCAATAAAAGTTCAAACAAGATTAAACAACATGCCCGCGC[A/G]
TACGCGCGGGCTACCTTCCTAGTTTTTATAATAAGTACATATACATATTAGACTAGTGACCAATCTATAAGTGCTTGTTGCTATTTTTAGAAGCTAAAGG
CCTTTAGCTTCTAAAAATAGCAACAAGCACTTATAGATTGGTCACTAGTCTAATATGTATATGTACTTATTATAAAAACTAGGAAGGTAGCCCGCGCGTA[T/C]
GCGCGGGCATGTTGTTTAATCTTGTTTGAACTTTTATTGCGAATGTTTATGTGTGGATCATATTTTTGAAATATTTGTTGACTCTATTTTAAACGTATTT
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 | 95.20% | 4.20% | 0.59% | 0.00% | NA |
All Indica | 2759 | 95.20% | 4.00% | 0.87% | 0.00% | NA |
All Japonica | 1512 | 99.70% | 0.20% | 0.13% | 0.00% | NA |
Aus | 269 | 69.50% | 30.10% | 0.37% | 0.00% | NA |
Indica I | 595 | 95.80% | 3.70% | 0.50% | 0.00% | NA |
Indica II | 465 | 95.10% | 4.50% | 0.43% | 0.00% | NA |
Indica III | 913 | 94.20% | 4.80% | 0.99% | 0.00% | NA |
Indica Intermediate | 786 | 95.90% | 2.80% | 1.27% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.20% | 0.40% | 0.40% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 93.30% | 5.60% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0222037003 | A -> G | LOC_Os02g36480.1 | downstream_gene_variant ; 2754.0bp to feature; MODIFIER | silent_mutation | Average:42.422; most accessible tissue: Callus, score: 60.857 | N | N | N | N |
vg0222037003 | A -> G | LOC_Os02g36490.1 | downstream_gene_variant ; 1601.0bp to feature; MODIFIER | silent_mutation | Average:42.422; most accessible tissue: Callus, score: 60.857 | N | N | N | N |
vg0222037003 | A -> G | LOC_Os02g36490.2 | downstream_gene_variant ; 1601.0bp to feature; MODIFIER | silent_mutation | Average:42.422; most accessible tissue: Callus, score: 60.857 | N | N | N | N |
vg0222037003 | A -> G | LOC_Os02g36490.3 | downstream_gene_variant ; 1601.0bp to feature; MODIFIER | silent_mutation | Average:42.422; most accessible tissue: Callus, score: 60.857 | N | N | N | N |
vg0222037003 | A -> G | LOC_Os02g36480-LOC_Os02g36490 | intergenic_region ; MODIFIER | silent_mutation | Average:42.422; most accessible tissue: Callus, score: 60.857 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0222037003 | 1.21E-06 | 1.21E-06 | mr1384 | Jap_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 |