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Detailed information for vg1014024679:

Variant ID: vg1014024679 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 14024679
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


ACCACAACAAATAAGCTACCCAACTTCTTAACTGTTTTCTCTAAAACAATACAACGCACTAATTGAATTTCTCATGTTTAAGAGGTGTATAGACAAGAAG[T/A]
CCTAAAGTCATGTGATGCTTTCATGTTCGACCTTGCTGGAGTTGTTTAGTGGCCAAATAATGAAATATGAGCAAGTGCTTTTCAGAAATGCTTCCTTCTT

Reverse complement sequence

AAGAAGGAAGCATTTCTGAAAAGCACTTGCTCATATTTCATTATTTGGCCACTAAACAACTCCAGCAAGGTCGAACATGAAAGCATCACATGACTTTAGG[A/T]
CTTCTTGTCTATACACCTCTTAAACATGAGAAATTCAATTAGTGCGTTGTATTGTTTTAGAGAAAACAGTTAAGAAGTTGGGTAGCTTATTTGTTGTGGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.10% 23.80% 0.06% 0.00% NA
All Indica  2759 59.40% 40.60% 0.07% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 42.70% 57.10% 0.17% 0.00% NA
Indica II  465 65.80% 34.20% 0.00% 0.00% NA
Indica III  913 64.80% 35.20% 0.00% 0.00% NA
Indica Intermediate  786 61.80% 38.00% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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% 8.90% 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
vg1014024679 T -> A LOC_Os10g26780-LOC_Os10g26800 intergenic_region ; MODIFIER silent_mutation Average:46.43; most accessible tissue: Callus, score: 79.312 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1014024679 NA 4.37E-06 mr1446 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
vg1014024679 6.44E-06 NA mr1577 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
vg1014024679 9.55E-06 1.65E-07 mr1577 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
vg1014024679 NA 2.02E-07 mr1734 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
vg1014024679 NA 1.21E-06 mr1780 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
vg1014024679 8.19E-07 6.81E-09 mr1792 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
vg1014024679 6.55E-06 4.92E-08 mr1792 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