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Detailed information for vg0621705457:

Variant ID: vg0621705457 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21705457
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: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CTGTGGGAGTAGTGGATTCGATGTGTATTTGTCCTACGTGGCGTATAAGGTTACTCAAATGAGGTGCTTGCACTGCTACTGCCCTAGAGGGTTCGTTTCC[A/G]
GATAGAATCAAGACCGATACCCTTCCGGTTTTGTATATAAATATGGCATGGCTGGTAGCTCCATGGATGGAGAAGACGATCTTGAGATTCAATGGAATTT

Reverse complement sequence

AAATTCCATTGAATCTCAAGATCGTCTTCTCCATCCATGGAGCTACCAGCCATGCCATATTTATATACAAAACCGGAAGGGTATCGGTCTTGATTCTATC[T/C]
GGAAACGAACCCTCTAGGGCAGTAGCAGTGCAAGCACCTCATTTGAGTAACCTTATACGCCACGTAGGACAAATACACATCGAATCCACTACTCCCACAG

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 90.90% 8.90% 0.21% 0.00% NA
All Indica  2759 91.50% 8.40% 0.07% 0.00% NA
All Japonica  1512 87.40% 12.00% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 94.80% 4.90% 0.22% 0.00% NA
Indica III  913 85.10% 14.80% 0.11% 0.00% NA
Indica Intermediate  786 90.60% 9.40% 0.00% 0.00% NA
Temperate Japonica  767 82.40% 16.70% 0.91% 0.00% NA
Tropical Japonica  504 92.10% 7.90% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 5.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0621705457 A -> G LOC_Os06g36840.1 upstream_gene_variant ; 2027.0bp to feature; MODIFIER silent_mutation Average:64.978; most accessible tissue: Callus, score: 85.473 N N N N
vg0621705457 A -> G LOC_Os06g36850.1 downstream_gene_variant ; 3494.0bp to feature; MODIFIER silent_mutation Average:64.978; most accessible tissue: Callus, score: 85.473 N N N N
vg0621705457 A -> G LOC_Os06g36840-LOC_Os06g36850 intergenic_region ; MODIFIER silent_mutation Average:64.978; most accessible tissue: Callus, score: 85.473 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621705457 NA 3.41E-07 mr1104 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
vg0621705457 NA 4.65E-06 mr1155 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
vg0621705457 1.38E-06 2.79E-07 mr1829 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
vg0621705457 2.33E-07 1.00E-07 mr1037_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
vg0621705457 NA 9.63E-06 mr1726_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
vg0621705457 NA 7.92E-08 mr1829_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