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Detailed information for vg0308122080:

Variant ID: vg0308122080 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8122080
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAATTTGATTAAAATTAAAATGATGCGACAGAAAAGTTAGTAGTTTATGTGTGCAGGAAAGTTTTGATGTGATAGAAAAGTTGAAAGTTTGAAGAAAA[A/G]
GTTGAAATCTAAACCAGGCTTATGTGTAGAAAAGTTTTGATGTGATAAAAAAGTTGAAAGTTCGATGAAAAAGTTGGAAACTAAACCAGGCCTATATATA

Reverse complement sequence

TATATATAGGCCTGGTTTAGTTTCCAACTTTTTCATCGAACTTTCAACTTTTTTATCACATCAAAACTTTTCTACACATAAGCCTGGTTTAGATTTCAAC[T/C]
TTTTCTTCAAACTTTCAACTTTTCTATCACATCAAAACTTTCCTGCACACATAAACTACTAACTTTTCTGTCGCATCATTTTAATTTTAATCAAATTTTC

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 95.20% 3.20% 1.63% 0.00% NA
All Indica  2759 91.90% 5.40% 2.72% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.00% 0.00% 4.03% 0.00% NA
Indica II  465 81.10% 12.50% 6.45% 0.00% NA
Indica III  913 96.50% 3.20% 0.33% 0.00% NA
Indica Intermediate  786 89.80% 7.90% 2.29% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 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
vg0308122080 A -> G LOC_Os03g14890.1 upstream_gene_variant ; 4338.0bp to feature; MODIFIER silent_mutation Average:54.072; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg0308122080 A -> G LOC_Os03g14890.2 upstream_gene_variant ; 4819.0bp to feature; MODIFIER silent_mutation Average:54.072; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg0308122080 A -> G LOC_Os03g14900.1 downstream_gene_variant ; 165.0bp to feature; MODIFIER silent_mutation Average:54.072; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N
vg0308122080 A -> G LOC_Os03g14890-LOC_Os03g14900 intergenic_region ; MODIFIER silent_mutation Average:54.072; most accessible tissue: Zhenshan97 panicle, score: 79.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308122080 NA 3.64E-07 mr1120_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
vg0308122080 NA 2.29E-06 mr1232_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
vg0308122080 NA 8.60E-06 mr1247_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