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Detailed information for vg0819798927:

Variant ID: vg0819798927 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19798927
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTTTAGAACTATCTTTCATAGTTATAAATGTTTATCATGCATGTCACTGTGTTTCATTTTGTATGTTTTTCACCCAAAAAACCGTCGAATGTTGTATA[G/A]
CTACTCCTAATGATAATATAAGTCTTCTGATGAAGAAATTCCCACTAATCCAGTAGATAATATTTTGTCCCACATAATCCATACCAGCCATGTCTCCTCA

Reverse complement sequence

TGAGGAGACATGGCTGGTATGGATTATGTGGGACAAAATATTATCTACTGGATTAGTGGGAATTTCTTCATCAGAAGACTTATATTATCATTAGGAGTAG[C/T]
TATACAACATTCGACGGTTTTTTGGGTGAAAAACATACAAAATGAAACACAGTGACATGCATGATAAACATTTATAACTATGAAAGATAGTTCTAAAAAC

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 85.40% 14.60% 0.00% 0.00% NA
All Indica  2759 75.30% 24.70% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 77.00% 23.00% 0.00% 0.00% NA
Indica II  465 95.90% 4.10% 0.00% 0.00% NA
Indica III  913 61.60% 38.40% 0.00% 0.00% NA
Indica Intermediate  786 77.90% 22.10% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0819798927 G -> A LOC_Os08g31930.1 intron_variant ; MODIFIER silent_mutation Average:33.946; most accessible tissue: Callus, score: 66.242 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819798927 NA 2.08E-07 mr1192 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
vg0819798927 NA 9.60E-09 mr1192 Ind_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
vg0819798927 NA 1.66E-08 mr1327_2 Ind_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
vg0819798927 NA 4.51E-07 mr1378_2 Ind_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