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Detailed information for vg1003124968:

Variant ID: vg1003124968 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3124968
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTTTGAACAACTTTTATATAGAAAATTTTCACACGAAACGCACTGTTTAGCAGTTTGAAAAGCATGCCACAAAAATCCAAAACTTTATCTCCCATGT[G/A]
TTGGGTTCTTAAACATGACCTTAGTAACTCCCTCCGTCCCAAAATATAACAACTTCGAGCCTCCAGATCTTTATCCCAAAATATAACAACTTCTACACCA

Reverse complement sequence

TGGTGTAGAAGTTGTTATATTTTGGGATAAAGATCTGGAGGCTCGAAGTTGTTATATTTTGGGACGGAGGGAGTTACTAAGGTCATGTTTAAGAACCCAA[C/T]
ACATGGGAGATAAAGTTTTGGATTTTTGTGGCATGCTTTTCAAACTGCTAAACAGTGCGTTTCGTGTGAAAATTTTCTATATAAAAGTTGTTCAAAATAT

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 76.80% 22.40% 0.83% 0.00% NA
All Indica  2759 62.30% 37.30% 0.36% 0.00% NA
All Japonica  1512 97.50% 0.90% 1.65% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 55.00% 44.50% 0.50% 0.00% NA
Indica II  465 74.60% 24.70% 0.65% 0.00% NA
Indica III  913 54.10% 45.70% 0.22% 0.00% NA
Indica Intermediate  786 70.10% 29.60% 0.25% 0.00% NA
Temperate Japonica  767 95.80% 1.30% 2.87% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 0.80% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 80.00% 15.60% 4.44% 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
vg1003124968 G -> A LOC_Os10g06140.1 intron_variant ; MODIFIER silent_mutation Average:32.286; most accessible tissue: Callus, score: 56.213 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003124968 1.50E-13 NA mr1538 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
vg1003124968 3.59E-12 1.12E-13 mr1538 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
vg1003124968 1.77E-21 4.07E-25 mr1547 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
vg1003124968 7.39E-17 1.42E-22 mr1547 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
vg1003124968 3.73E-44 1.13E-55 mr1709 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
vg1003124968 7.14E-43 1.05E-67 mr1709 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
vg1003124968 4.44E-12 NA mr1538_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
vg1003124968 6.56E-15 4.48E-21 mr1538_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
vg1003124968 1.23E-18 1.30E-24 mr1547_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
vg1003124968 1.13E-20 6.39E-29 mr1547_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
vg1003124968 1.91E-60 1.74E-92 mr1709_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
vg1003124968 8.26E-64 2.46E-108 mr1709_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