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Detailed information for vg0421499528:

Variant ID: vg0421499528 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21499528
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, T: 0.12, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


ACTGCCATCACATTGGTGCTGCTCGCAGCCTTCTATGGACAGCTACCGTCACATTCGGTTCAAAACCCCTGGTCCATAGTTTTTTTTTTTTCACTTACCC[G/T]
GTTTTTAGCTTGTTCTTTAAGGTTTTTTTAAAATAAAAAAAATCACATATTCTCAAAAAATCATTTTATTTTCAAATTGGAAGTTGAACTTAACTTATAT

Reverse complement sequence

ATATAAGTTAAGTTCAACTTCCAATTTGAAAATAAAATGATTTTTTGAGAATATGTGATTTTTTTTATTTTAAAAAAACCTTAAAGAACAAGCTAAAAAC[C/A]
GGGTAAGTGAAAAAAAAAAAACTATGGACCAGGGGTTTTGAACCGAATGTGACGGTAGCTGTCCATAGAAGGCTGCGAGCAGCACCAATGTGATGGCAGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.40% 33.20% 0.28% 3.15% NA
All Indica  2759 66.00% 29.40% 0.25% 4.35% NA
All Japonica  1512 61.80% 38.00% 0.13% 0.00% NA
Aus  269 54.30% 34.20% 0.74% 10.78% NA
Indica I  595 82.00% 17.80% 0.17% 0.00% NA
Indica II  465 78.10% 21.50% 0.00% 0.43% NA
Indica III  913 49.50% 42.30% 0.44% 7.78% NA
Indica Intermediate  786 66.00% 27.70% 0.25% 5.98% NA
Temperate Japonica  767 77.20% 22.60% 0.26% 0.00% NA
Tropical Japonica  504 27.20% 72.80% 0.00% 0.00% NA
Japonica Intermediate  241 85.50% 14.50% 0.00% 0.00% NA
VI/Aromatic  96 41.70% 56.20% 2.08% 0.00% NA
Intermediate  90 56.70% 43.30% 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
vg0421499528 G -> DEL N N silent_mutation Average:37.585; most accessible tissue: Callus, score: 79.53 N N N N
vg0421499528 G -> T LOC_Os04g35340-LOC_Os04g35370 intergenic_region ; MODIFIER silent_mutation Average:37.585; most accessible tissue: Callus, score: 79.53 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421499528 NA 8.51E-06 mr1277 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
vg0421499528 2.04E-06 NA mr1829 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
vg0421499528 NA 3.87E-06 mr1346_2 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
vg0421499528 NA 2.32E-07 mr1707_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
vg0421499528 4.07E-06 NA mr1721_2 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
vg0421499528 1.15E-07 NA mr1829_2 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
vg0421499528 1.15E-06 NA mr1902_2 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