Variant ID: vg0116735143 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 16735143 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGGTGTTTGGAAAAATAAAAACAAAAGTGGTAAAAAGCACACTTCGTACAAACGTACACATTGTGCTCAAAAATCCAAAAGAAAACTTCTCCCCCTTTTT[A/T]
AAAGAAAGAAATTCCCAAAAACATGCTTTTCTCAAAAACTCTCAAAAATCCAAAAGAAAACTTCTTCCCCTTTTTAAAAGAAAGAAATTCCCAATTGAAC
GTTCAATTGGGAATTTCTTTCTTTTAAAAAGGGGAAGAAGTTTTCTTTTGGATTTTTGAGAGTTTTTGAGAAAAGCATGTTTTTGGGAATTTCTTTCTTT[T/A]
AAAAAGGGGGAGAAGTTTTCTTTTGGATTTTTGAGCACAATGTGTACGTTTGTACGAAGTGTGCTTTTTACCACTTTTGTTTTTATTTTTCCAAACACCA
Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 99.10% | 0.70% | 0.21% | 0.00% | NA |
All Indica | 2759 | 98.80% | 0.90% | 0.25% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 96.70% | 2.20% | 1.12% | 0.00% | NA |
Indica I | 595 | 96.80% | 2.50% | 0.67% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 98.70% | 1.00% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 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 | 100.00% | 0.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0116735143 | A -> T | LOC_Os01g29860.1 | upstream_gene_variant ; 4234.0bp to feature; MODIFIER | silent_mutation | Average:20.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
vg0116735143 | A -> T | LOC_Os01g29870.1 | downstream_gene_variant ; 1424.0bp to feature; MODIFIER | silent_mutation | Average:20.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
vg0116735143 | A -> T | LOC_Os01g29880.1 | downstream_gene_variant ; 3918.0bp to feature; MODIFIER | silent_mutation | Average:20.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
vg0116735143 | A -> T | LOC_Os01g29870-LOC_Os01g29880 | intergenic_region ; MODIFIER | silent_mutation | Average:20.671; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0116735143 | NA | 1.33E-06 | mr1042 | 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 |
vg0116735143 | NA | 8.24E-07 | mr1043 | 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 |
vg0116735143 | NA | 5.82E-08 | mr1739 | 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 |