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Detailed information for vg0506492322:

Variant ID: vg0506492322 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6492322
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTGCATATGTTAAAGTTTTACAATACTAAGGGTTTTACAATAATAGGTACTCACCTAACTAATTAATACACAGCGGAAGTTTCTATACATTCTGACTAG[G/A]
AAGGTATAATATTTAAGGATTCTCTAAGTTATCGGGGTCATCGTAGTAATAGTCATAAGGGTCCTCCTCTTGACCCAAATCTGAAAAAGGGGTTATAAGA

Reverse complement sequence

TCTTATAACCCCTTTTTCAGATTTGGGTCAAGAGGAGGACCCTTATGACTATTACTACGATGACCCCGATAACTTAGAGAATCCTTAAATATTATACCTT[C/T]
CTAGTCAGAATGTATAGAAACTTCCGCTGTGTATTAATTAGTTAGGTGAGTACCTATTATTGTAAAACCCTTAGTATTGTAAAACTTTAACATATGCAAT

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 93.80% 6.00% 0.23% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 81.60% 17.70% 0.73% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 52.60% 46.80% 0.60% 0.00% NA
Japonica Intermediate  241 86.30% 10.40% 3.32% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0506492322 G -> A LOC_Os05g11470.1 downstream_gene_variant ; 1337.0bp to feature; MODIFIER silent_mutation Average:43.564; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0506492322 G -> A LOC_Os05g11470-LOC_Os05g11490 intergenic_region ; MODIFIER silent_mutation Average:43.564; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506492322 1.03E-06 1.03E-06 mr1848 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
vg0506492322 NA 5.56E-06 mr1124_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
vg0506492322 1.90E-06 2.40E-06 mr1850_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