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Detailed information for vg0334550767:

Variant ID: vg0334550767 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34550767
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGTGTGGGTGTGTCATCTAGGTCCCTAAACTCTCAAAATGCATTTTCGGATCCTTGAACTTGTTTTGGGGTGTCATACAAGTCCAAACGAGCTCCAACC[C/A]
CTTCCATGCGCTGATGTGGCATGCCACGATAGTTCATACGTGTTAGTTGGACCCACGTATCAGTCACATAGAAAAAAAATATAATTAGAAAAATATATTT

Reverse complement sequence

AAATATATTTTTCTAATTATATTTTTTTTCTATGTGACTGATACGTGGGTCCAACTAACACGTATGAACTATCGTGGCATGCCACATCAGCGCATGGAAG[G/T]
GGTTGGAGCTCGTTTGGACTTGTATGACACCCCAAAACAAGTTCAAGGATCCGAAAATGCATTTTGAGAGTTTAGGGACCTAGATGACACACCCACACAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.20% 42.60% 0.23% 0.00% NA
All Indica  2759 93.80% 5.90% 0.33% 0.00% NA
All Japonica  1512 0.90% 99.00% 0.07% 0.00% NA
Aus  269 21.60% 78.40% 0.00% 0.00% NA
Indica I  595 99.20% 0.20% 0.67% 0.00% NA
Indica II  465 93.80% 6.00% 0.22% 0.00% NA
Indica III  913 92.60% 7.40% 0.00% 0.00% NA
Indica Intermediate  786 91.20% 8.30% 0.51% 0.00% NA
Temperate Japonica  767 1.00% 98.80% 0.13% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 45.60% 53.30% 1.11% 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
vg0334550767 C -> A LOC_Os03g60810.1 upstream_gene_variant ; 2657.0bp to feature; MODIFIER silent_mutation Average:52.718; most accessible tissue: Callus, score: 79.951 N N N N
vg0334550767 C -> A LOC_Os03g60800.1 downstream_gene_variant ; 4616.0bp to feature; MODIFIER silent_mutation Average:52.718; most accessible tissue: Callus, score: 79.951 N N N N
vg0334550767 C -> A LOC_Os03g60820.1 downstream_gene_variant ; 3875.0bp to feature; MODIFIER silent_mutation Average:52.718; most accessible tissue: Callus, score: 79.951 N N N N
vg0334550767 C -> A LOC_Os03g60810-LOC_Os03g60820 intergenic_region ; MODIFIER silent_mutation Average:52.718; most accessible tissue: Callus, score: 79.951 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334550767 1.54E-07 NA mr1151 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
vg0334550767 NA 2.08E-09 mr1342 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
vg0334550767 NA 2.20E-24 mr1551 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