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Detailed information for vg1021465447:

Variant ID: vg1021465447 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 21465447
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTGTAATGTTACTATCTCCTCTTCAAAATATTAGTTTACTGGCTCATCATGTAGTGTTACTATCTTTGTCTCAAGATAGTACGATAGAATAACGAATCT[G/A,T]
AACAGTGTCTAAATCCATGGCGATGGAGTAACTGTGAAGCTCATCCATGATCTATGGCGATCGATCGATTAATTGGTTGAGTTTTGTTTTTTTCCAGGTG

Reverse complement sequence

CACCTGGAAAAAAACAAAACTCAACCAATTAATCGATCGATCGCCATAGATCATGGATGAGCTTCACAGTTACTCCATCGCCATGGATTTAGACACTGTT[C/T,A]
AGATTCGTTATTCTATCGTACTATCTTGAGACAAAGATAGTAACACTACATGATGAGCCAGTAAACTAATATTTTGAAGAGGAGATAGTAACATTACACG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.40% 3.20% 0.36% 0.00% T: 0.04%
All Indica  2759 94.00% 5.40% 0.58% 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 97.80% 1.30% 0.84% 0.00% NA
Indica II  465 76.60% 21.90% 1.51% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 4.80% 0.51% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 4.40% 1.11% 0.00% T: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1021465447 G -> T LOC_Os10g40080.1 upstream_gene_variant ; 2112.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021465447 G -> T LOC_Os10g40070.1 downstream_gene_variant ; 4792.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021465447 G -> T LOC_Os10g40100.1 downstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021465447 G -> T LOC_Os10g40100.2 downstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021465447 G -> T LOC_Os10g40090.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021465447 G -> A LOC_Os10g40080.1 upstream_gene_variant ; 2112.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021465447 G -> A LOC_Os10g40070.1 downstream_gene_variant ; 4792.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021465447 G -> A LOC_Os10g40100.1 downstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021465447 G -> A LOC_Os10g40100.2 downstream_gene_variant ; 2161.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg1021465447 G -> A LOC_Os10g40090.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1021465447 2.45E-06 2.45E-06 mr1392 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