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Detailed information for vg0621807445:

Variant ID: vg0621807445 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21807445
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.51, A: 0.49, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


CCTTGGGATTCTTACCACCCTATTGGTTTGAGACATTCTTTGTCAAGTTTGACATATATCCTTATGTATTAGGGACATCTATATGCAAAAAGTTTGAGTG[G/A]
TTTGGTAGGCAACGACAAAATCAACATGATAAATGTATTTTGGATGTCAAATCGTGCCCATGGAGAATGTGGCACATTTTGACAAATATGCTTGTAAAAG

Reverse complement sequence

CTTTTACAAGCATATTTGTCAAAATGTGCCACATTCTCCATGGGCACGATTTGACATCCAAAATACATTTATCATGTTGATTTTGTCGTTGCCTACCAAA[C/T]
CACTCAAACTTTTTGCATATAGATGTCCCTAATACATAAGGATATATGTCAAACTTGACAAAGAATGTCTCAAACCAATAGGGTGGTAAGAATCCCAAGG

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 75.70% 24.30% 0.04% 0.00% NA
All Indica  2759 81.00% 19.00% 0.00% 0.00% NA
All Japonica  1512 79.40% 20.50% 0.13% 0.00% NA
Aus  269 3.00% 97.00% 0.00% 0.00% NA
Indica I  595 96.30% 3.70% 0.00% 0.00% NA
Indica II  465 80.00% 20.00% 0.00% 0.00% NA
Indica III  913 70.90% 29.10% 0.00% 0.00% NA
Indica Intermediate  786 81.80% 18.20% 0.00% 0.00% NA
Temperate Japonica  767 79.90% 19.90% 0.13% 0.00% NA
Tropical Japonica  504 77.40% 22.40% 0.20% 0.00% NA
Japonica Intermediate  241 81.70% 18.30% 0.00% 0.00% NA
VI/Aromatic  96 67.70% 32.30% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0621807445 G -> A LOC_Os06g36990.1 upstream_gene_variant ; 1983.0bp to feature; MODIFIER silent_mutation Average:51.282; most accessible tissue: Callus, score: 83.27 N N N N
vg0621807445 G -> A LOC_Os06g36980-LOC_Os06g36990 intergenic_region ; MODIFIER silent_mutation Average:51.282; most accessible tissue: Callus, score: 83.27 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621807445 NA 7.80E-06 mr1382 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
vg0621807445 3.02E-06 NA mr1398 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
vg0621807445 NA 1.75E-07 mr1057_2 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
vg0621807445 NA 1.15E-08 mr1126_2 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
vg0621807445 NA 7.20E-06 mr1827_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