Variant ID: vg0112163580 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 12163580 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTGTACCGCAGACACCGTGGGTTAATTACTATGGATGAAAACGATACGGAAATTTTCAACCATACCAGCATATTCTGATTATAAAATCTCACTACTATAC[A/T]
TGCTTTTTTTAATACGGCCAAAACACATTTTTGCAGGCAGGCACTTTGCCCACCGTGTTTGGGAAAATTAGAAATTTTCCAGGCAGGCAACCAAACCACA
TGTGGTTTGGTTGCCTGCCTGGAAAATTTCTAATTTTCCCAAACACGGTGGGCAAAGTGCCTGCCTGCAAAAATGTGTTTTGGCCGTATTAAAAAAAGCA[T/A]
GTATAGTAGTGAGATTTTATAATCAGAATATGCTGGTATGGTTGAAAATTTCCGTATCGTTTTCATCCATAGTAATTAACCCACGGTGTCTGCGGTACAC
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 | 94.90% | 2.20% | 2.92% | 0.00% | NA |
All Indica | 2759 | 91.60% | 3.70% | 4.71% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.07% | 0.00% | NA |
Aus | 269 | 98.90% | 0.00% | 1.12% | 0.00% | NA |
Indica I | 595 | 77.50% | 8.10% | 14.45% | 0.00% | NA |
Indica II | 465 | 97.20% | 0.00% | 2.80% | 0.00% | NA |
Indica III | 913 | 95.60% | 4.10% | 0.33% | 0.00% | NA |
Indica Intermediate | 786 | 94.30% | 2.20% | 3.56% | 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 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 0.00% | 4.44% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0112163580 | A -> T | LOC_Os01g21670.1 | upstream_gene_variant ; 1812.0bp to feature; MODIFIER | silent_mutation | Average:34.919; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 | N | N | N | N |
vg0112163580 | A -> T | LOC_Os01g21690.1 | upstream_gene_variant ; 3153.0bp to feature; MODIFIER | silent_mutation | Average:34.919; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 | N | N | N | N |
vg0112163580 | A -> T | LOC_Os01g21680.1 | downstream_gene_variant ; 190.0bp to feature; MODIFIER | silent_mutation | Average:34.919; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 | N | N | N | N |
vg0112163580 | A -> T | LOC_Os01g21670-LOC_Os01g21680 | intergenic_region ; MODIFIER | silent_mutation | Average:34.919; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0112163580 | NA | 2.73E-06 | mr1726_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 |
vg0112163580 | NA | 5.39E-07 | mr1927_2 | 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 |