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Detailed information for vg0400215181:

Variant ID: vg0400215181 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 215181
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGATTCAGGAGGAAATTAGGGCCCCTTTAAATCACGGGATTAAAAAAATGGAGGAATAGGAAAAACATACGATTCTGATAGGAATTGAAGTTTAAAACA[G/A]
AGGATTGCAAAACACAGAAAAAACACAGGAATGGTCGTTTGATTGGAACGCAGGAAAAACACAGGAATCGGATGAGAGAGATAGACTCAAAGGAAATTTT

Reverse complement sequence

AAAATTTCCTTTGAGTCTATCTCTCTCATCCGATTCCTGTGTTTTTCCTGCGTTCCAATCAAACGACCATTCCTGTGTTTTTTCTGTGTTTTGCAATCCT[C/T]
TGTTTTAAACTTCAATTCCTATCAGAATCGTATGTTTTTCCTATTCCTCCATTTTTTTAATCCCGTGATTTAAAGGGGCCCTAATTTCCTCCTGAATCAA

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 95.40% 4.40% 0.06% 0.11% NA
All Indica  2759 92.40% 7.30% 0.11% 0.18% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 87.90% 11.90% 0.17% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 92.60% 6.80% 0.11% 0.55% NA
Indica Intermediate  786 93.00% 6.90% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0400215181 G -> DEL N N silent_mutation Average:45.124; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0400215181 G -> A LOC_Os04g01280.1 upstream_gene_variant ; 748.0bp to feature; MODIFIER silent_mutation Average:45.124; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0400215181 G -> A LOC_Os04g01290.1 downstream_gene_variant ; 4342.0bp to feature; MODIFIER silent_mutation Average:45.124; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0400215181 G -> A LOC_Os04g01290.2 downstream_gene_variant ; 4342.0bp to feature; MODIFIER silent_mutation Average:45.124; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0400215181 G -> A LOC_Os04g01290.3 downstream_gene_variant ; 4342.0bp to feature; MODIFIER silent_mutation Average:45.124; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0400215181 G -> A LOC_Os04g01270-LOC_Os04g01280 intergenic_region ; MODIFIER silent_mutation Average:45.124; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0400215181 3.45E-07 3.45E-07 mr1756 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
vg0400215181 2.80E-06 2.58E-08 mr1976 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