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Detailed information for vg0200926863:

Variant ID: vg0200926863 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 926863
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


GAAGTGAAGCTGTACTCTGAATTAAGATTGTGTAAACACAGCATATAAAAGGTTGCATACAGATATGCAGTATTTCAAAAATACATGAAAAATAGTCCAA[A/G]
TATTTTCTGTAAGAACTATAACTACAAGAAAGACTATAATTTTAAGCAACTTTGGCAAAAGTACCTTCAATGTGATGCTAGAGCCAAACCAAACATCACC

Reverse complement sequence

GGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGGTACTTTTGCCAAAGTTGCTTAAAATTATAGTCTTTCTTGTAGTTATAGTTCTTACAGAAAATA[T/C]
TTGGACTATTTTTCATGTATTTTTGAAATACTGCATATCTGTATGCAACCTTTTATATGCTGTGTTTACACAATCTTAATTCAGAGTACAGCTTCACTTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 2.20% 1.84% 0.00% NA
All Indica  2759 99.80% 0.00% 0.22% 0.00% NA
All Japonica  1512 88.00% 6.90% 5.16% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.00% 0.86% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 83.10% 9.00% 7.95% 0.00% NA
Tropical Japonica  504 98.80% 0.20% 0.99% 0.00% NA
Japonica Intermediate  241 80.90% 14.10% 4.98% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0200926863 A -> G LOC_Os02g02540.1 downstream_gene_variant ; 2893.0bp to feature; MODIFIER silent_mutation Average:43.622; most accessible tissue: Minghui63 flower, score: 56.131 N N N N
vg0200926863 A -> G LOC_Os02g02550.1 downstream_gene_variant ; 231.0bp to feature; MODIFIER silent_mutation Average:43.622; most accessible tissue: Minghui63 flower, score: 56.131 N N N N
vg0200926863 A -> G LOC_Os02g02570.1 downstream_gene_variant ; 3389.0bp to feature; MODIFIER silent_mutation Average:43.622; most accessible tissue: Minghui63 flower, score: 56.131 N N N N
vg0200926863 A -> G LOC_Os02g02560.1 intron_variant ; MODIFIER silent_mutation Average:43.622; most accessible tissue: Minghui63 flower, score: 56.131 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200926863 NA 6.19E-06 mr1201 Jap_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
vg0200926863 1.03E-06 2.87E-07 mr1274 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