Variant ID: vg0719509692 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 19509692 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 236. )
AATTTTGACACCTATTTATAGTTGTTTATAGTAGCTCTTACATATTCATCTTACGACTTTGATTATCCGTTGATCCCTAATTTACTAATCACCATGACTC[G/A]
CATAAAAAAATATGTACTACATAGAGTTTAGGACAGCTGAAATTGATAAATTATCTGATTTATGTGATAGCTATTTGAGGGTATAAACGAATGAATTGAC
GTCAATTCATTCGTTTATACCCTCAAATAGCTATCACATAAATCAGATAATTTATCAATTTCAGCTGTCCTAAACTCTATGTAGTACATATTTTTTTATG[C/T]
GAGTCATGGTGATTAGTAAATTAGGGATCAACGGATAATCAAAGTCGTAAGATGAATATGTAAGAGCTACTATAAACAACTATAAATAGGTGTCAAAATT
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 | 90.70% | 9.30% | 0.00% | 0.00% | NA |
All Indica | 2759 | 86.70% | 13.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 75.50% | 24.50% | 0.00% | 0.00% | NA |
Indica I | 595 | 92.80% | 7.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
Indica III | 913 | 77.50% | 22.50% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 85.10% | 14.90% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.70% | 0.30% | 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 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 2.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0719509692 | G -> A | LOC_Os07g32670.1 | downstream_gene_variant ; 4533.0bp to feature; MODIFIER | silent_mutation | Average:26.585; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
vg0719509692 | G -> A | LOC_Os07g32670-LOC_Os07g32680 | intergenic_region ; MODIFIER | silent_mutation | Average:26.585; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0719509692 | 6.65E-07 | NA | mr1248_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 |
vg0719509692 | NA | 6.63E-06 | mr1406_2 | 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 |
vg0719509692 | 6.59E-06 | NA | mr1423_2 | 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 |
vg0719509692 | 8.66E-06 | NA | mr1800_2 | 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 |