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Detailed information for vg0805104035:

Variant ID: vg0805104035 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5104035
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAGAGCCATAGGCTTGTTACAGCTACTCCAAGAATGTTGAGAATATGAGATCGTGGCCAGGGCGATGAAATCCCTAAAAAGTGTTGAAAGGTTGGACTA[G/A]
TTATTAATTGCCAAGTTCTTACATGATTTGCATATTGCTTCGCTAGCTATACCAAGATCATGAGGCGAATTCCCAATCATATTGCAATACGCGGAACAAA

Reverse complement sequence

TTTGTTCCGCGTATTGCAATATGATTGGGAATTCGCCTCATGATCTTGGTATAGCTAGCGAAGCAATATGCAAATCATGTAAGAACTTGGCAATTAATAA[C/T]
TAGTCCAACCTTTCAACACTTTTTAGGGATTTCATCGCCCTGGCCACGATCTCATATTCTCAACATTCTTGGAGTAGCTGTAACAAGCCTATGGCTCTGT

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 96.50% 3.50% 0.04% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 89.40% 10.40% 0.13% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 80.60% 19.40% 0.00% 0.00% NA
Japonica Intermediate  241 81.70% 17.40% 0.83% 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
vg0805104035 G -> A LOC_Os08g08800.1 downstream_gene_variant ; 4633.0bp to feature; MODIFIER silent_mutation Average:58.545; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg0805104035 G -> A LOC_Os08g08810.1 downstream_gene_variant ; 3577.0bp to feature; MODIFIER silent_mutation Average:58.545; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg0805104035 G -> A LOC_Os08g08800-LOC_Os08g08810 intergenic_region ; MODIFIER silent_mutation Average:58.545; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805104035 6.37E-07 5.41E-09 mr1227 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
vg0805104035 NA 2.19E-06 mr1556_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
vg0805104035 NA 2.45E-06 mr1764_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