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Detailed information for vg0621048541:

Variant ID: vg0621048541 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21048541
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATTCCTGATCGACCAAAACGCCTTTTTCGTATATGGAGTACAGTTTCCGACCATATCGTTTTTTATCTATTTATAAATTTTGTTTTTTCTAATTTTTT[G/A]
TGCATCATATTAATGTCGACACTAAGTAGTTTAAATAATAAATATATATAATCAATTACCGGTCGATCGAGCTTCGTTTCCTAGGAGATGCCCGTTTTCA

Reverse complement sequence

TGAAAACGGGCATCTCCTAGGAAACGAAGCTCGATCGACCGGTAATTGATTATATATATTTATTATTTAAACTACTTAGTGTCGACATTAATATGATGCA[C/T]
AAAAAATTAGAAAAAACAAAATTTATAAATAGATAAAAAACGATATGGTCGGAAACTGTACTCCATATACGAAAAAGGCGTTTTGGTCGATCAGGAATTT

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 88.00% 10.60% 1.46% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 64.00% 31.60% 4.37% 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 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 81.70% 12.50% 5.74% 0.00% NA
Tropical Japonica  504 39.90% 57.90% 2.18% 0.00% NA
Japonica Intermediate  241 58.10% 37.30% 4.56% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 81.10% 15.60% 3.33% 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
vg0621048541 G -> A LOC_Os06g36010.1 downstream_gene_variant ; 181.0bp to feature; MODIFIER silent_mutation Average:57.073; most accessible tissue: Callus, score: 81.365 N N N N
vg0621048541 G -> A LOC_Os06g36000-LOC_Os06g36010 intergenic_region ; MODIFIER silent_mutation Average:57.073; most accessible tissue: Callus, score: 81.365 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621048541 NA 2.29E-10 mr1648 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
vg0621048541 NA 5.32E-06 mr1648 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
vg0621048541 1.61E-08 NA mr1758 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
vg0621048541 NA 7.45E-11 mr1905 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