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Detailed information for vg0324083524:

Variant ID: vg0324083524 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24083524
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGTATGTTTACGTGGCGTTCCCAAGAAAATAGTGTCAGACAGAGGTAGTCAGTATACTTCGAAGTTTTGGCAGAAGTTACAAGAAGAGATGGGTACTC[G/A]
TTTGAATTTCAGTACTGCCTATAACCCTCAAACTGATGGTCAGACAGAAAGAGTGAATCAAATTTTACAAGACATGGTTAGAGCCTGTGTCCTAGATTTC

Reverse complement sequence

GAAATCTAGGACACAGGCTCTAACCATGTCTTGTAAAATTTGATTCACTCTTTCTGTCTGACCATCAGTTTGAGGGTTATAGGCAGTACTGAAATTCAAA[C/T]
GAGTACCCATCTCTTCTTGTAACTTCTGCCAAAACTTCGAAGTATACTGACTACCTCTGTCTGACACTATTTTCTTGGGAACGCCACGTAAACATACAAC

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 95.20% 3.20% 1.63% 0.00% NA
All Indica  2759 99.70% 0.20% 0.14% 0.00% NA
All Japonica  1512 85.70% 9.50% 4.83% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.50% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 73.00% 18.50% 8.47% 0.00% NA
Tropical Japonica  504 99.20% 0.00% 0.79% 0.00% NA
Japonica Intermediate  241 97.90% 0.40% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0324083524 G -> A LOC_Os03g43169.1 upstream_gene_variant ; 524.0bp to feature; MODIFIER silent_mutation Average:9.681; most accessible tissue: Callus, score: 43.517 N N N N
vg0324083524 G -> A LOC_Os03g43160.1 downstream_gene_variant ; 699.0bp to feature; MODIFIER silent_mutation Average:9.681; most accessible tissue: Callus, score: 43.517 N N N N
vg0324083524 G -> A LOC_Os03g43180.1 downstream_gene_variant ; 1549.0bp to feature; MODIFIER silent_mutation Average:9.681; most accessible tissue: Callus, score: 43.517 N N N N
vg0324083524 G -> A LOC_Os03g43190.1 downstream_gene_variant ; 3555.0bp to feature; MODIFIER silent_mutation Average:9.681; most accessible tissue: Callus, score: 43.517 N N N N
vg0324083524 G -> A LOC_Os03g43160-LOC_Os03g43169 intergenic_region ; MODIFIER silent_mutation Average:9.681; most accessible tissue: Callus, score: 43.517 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324083524 4.37E-06 NA mr1570 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
vg0324083524 2.45E-06 1.41E-07 mr1570 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