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Detailed information for vg0626730824:

Variant ID: vg0626730824 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 26730824
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.08, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GACATTTATATGGAGCAACCTGAAGGTTTTGTTGTTCCTGGAAAAGAGAACCTAGTATGTAGGTTAAAGAAATCTCTTTATGGATTGAAGCAGTCACCTA[G/A]
ACAATAGTATAAGAGATTTGACTCTTTCATGCTTTCTCAGAAGTTTAGAAGATCCAATTATGATAGCTGTGTTTATCTCAAAGTTGTTGATGGTTTAGCT

Reverse complement sequence

AGCTAAACCATCAACAACTTTGAGATAAACACAGCTATCATAATTGGATCTTCTAAACTTCTGAGAAAGCATGAAAGAGTCAAATCTCTTATACTATTGT[C/T]
TAGGTGACTGCTTCAATCCATAAAGAGATTTCTTTAACCTACATACTAGGTTCTCTTTTCCAGGAACAACAAAACCTTCAGGTTGCTCCATATAAATGTC

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 65.10% 34.70% 0.23% 0.00% NA
All Indica  2759 43.20% 56.40% 0.36% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 79.20% 20.80% 0.00% 0.00% NA
Indica I  595 30.90% 69.10% 0.00% 0.00% NA
Indica II  465 21.70% 77.60% 0.65% 0.00% NA
Indica III  913 56.80% 42.80% 0.33% 0.00% NA
Indica Intermediate  786 49.50% 50.00% 0.51% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 80.00% 18.90% 1.11% 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
vg0626730824 G -> A LOC_Os06g44290.1 intron_variant ; MODIFIER silent_mutation Average:26.03; most accessible tissue: Minghui63 young leaf, score: 36.684 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0626730824 2.95E-06 NA mr1064 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
vg0626730824 1.01E-07 1.36E-09 mr1064 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
vg0626730824 3.33E-06 NA mr1534 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
vg0626730824 4.47E-07 2.78E-08 mr1534 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
vg0626730824 NA 2.32E-06 mr1349_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