Variant ID: vg0222034653 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 22034653 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCAGCTCTTTATTTATACTACACTTCTTTTATGTTATGAGTGTCTTATTTGTTCTTTGTGATGTGATGTTGATTTTATCCTTTTGAGTGCTCACCATGTC[G/A]
TATCTTTTGCATATCATATCTATTCTTACTGCTTATTTGCATCCCAGATGAAGGAAACTCTCTTCGGTTGCTCCCATTAATATATGCATATGAGCTTCAC
GTGAAGCTCATATGCATATATTAATGGGAGCAACCGAAGAGAGTTTCCTTCATCTGGGATGCAAATAAGCAGTAAGAATAGATATGATATGCAAAAGATA[C/T]
GACATGGTGAGCACTCAAAAGGATAAAATCAACATCACATCACAAAGAACAAATAAGACACTCATAACATAAAAGAAGTGTAGTATAAATAAAGAGCTGC
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 | 62.80% | 37.00% | 0.15% | 0.00% | NA |
All Indica | 2759 | 91.70% | 8.00% | 0.25% | 0.00% | NA |
All Japonica | 1512 | 8.10% | 91.90% | 0.00% | 0.00% | NA |
Aus | 269 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
Indica I | 595 | 95.60% | 4.20% | 0.17% | 0.00% | NA |
Indica II | 465 | 97.20% | 2.40% | 0.43% | 0.00% | NA |
Indica III | 913 | 90.40% | 9.40% | 0.22% | 0.00% | NA |
Indica Intermediate | 786 | 87.20% | 12.60% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 1.30% | 98.70% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 19.80% | 80.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 5.00% | 95.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 13.50% | 86.50% | 0.00% | 0.00% | NA |
Intermediate | 90 | 52.20% | 47.80% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0222034653 | G -> A | LOC_Os02g36470.1 | downstream_gene_variant ; 2956.0bp to feature; MODIFIER | silent_mutation | Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
vg0222034653 | G -> A | LOC_Os02g36480.1 | downstream_gene_variant ; 404.0bp to feature; MODIFIER | silent_mutation | Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
vg0222034653 | G -> A | LOC_Os02g36490.1 | downstream_gene_variant ; 3951.0bp to feature; MODIFIER | silent_mutation | Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
vg0222034653 | G -> A | LOC_Os02g36490.2 | downstream_gene_variant ; 3951.0bp to feature; MODIFIER | silent_mutation | Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
vg0222034653 | G -> A | LOC_Os02g36490.3 | downstream_gene_variant ; 3951.0bp to feature; MODIFIER | silent_mutation | Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
vg0222034653 | G -> A | LOC_Os02g36480-LOC_Os02g36490 | intergenic_region ; MODIFIER | silent_mutation | Average:19.399; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0222034653 | 4.78E-06 | 4.01E-06 | mr1911_2 | 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 |