\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0204941081:

Variant ID: vg0204941081 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4941081
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTGTTGTGTTGGTCACTTGGTTGCTCAGATTCGGTGGAAGGAAATATGTTTCTATTTTTTGGTGGTTCTTGTAATTTCTGGGTAGATGTTACTGTTC[T/A]
GAGTTCAATTGCTCATCAAGCTGTATTTTTTTCAGGAAAACATGCTGATTTTTTTATCAGGAAAGTTGTGTAATTTTGATGATTTAGGTGGCTCTTGTAA

Reverse complement sequence

TTACAAGAGCCACCTAAATCATCAAAATTACACAACTTTCCTGATAAAAAAATCAGCATGTTTTCCTGAAAAAAATACAGCTTGATGAGCAATTGAACTC[A/T]
GAACAGTAACATCTACCCAGAAATTACAAGAACCACCAAAAAATAGAAACATATTTCCTTCCACCGAATCTGAGCAACCAAGTGACCAACACAACAATAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.00% 1.50% 1.57% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 90.70% 4.60% 4.76% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 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 84.90% 6.60% 8.47% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 7.10% 2.90% 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

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0204941081 T -> A LOC_Os02g09590.1 upstream_gene_variant ; 3275.0bp to feature; MODIFIER silent_mutation Average:39.835; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0204941081 T -> A LOC_Os02g09610.1 upstream_gene_variant ; 1681.0bp to feature; MODIFIER silent_mutation Average:39.835; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0204941081 T -> A LOC_Os02g09620.1 upstream_gene_variant ; 3579.0bp to feature; MODIFIER silent_mutation Average:39.835; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0204941081 T -> A LOC_Os02g09600.1 intron_variant ; MODIFIER silent_mutation Average:39.835; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0204941081 T -> A LOC_Os02g09600.3 intron_variant ; MODIFIER silent_mutation Average:39.835; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg0204941081 T -> A LOC_Os02g09600.2 intron_variant ; MODIFIER silent_mutation Average:39.835; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204941081 NA 1.07E-06 mr1057 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
vg0204941081 2.30E-06 2.30E-06 mr1609 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
vg0204941081 NA 7.50E-06 mr1057_2 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