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Detailed information for vg0328947114:

Variant ID: vg0328947114 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 28947114
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.06, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGCACATGTTTAACCGTTCGTCTTATTTAAAAACTTTTGTGAGATATGTAAAATTATATGCCTACATAAAAATATATTTAACAATGAATCAAATGATA[A/G]
AAAAAGAATTAATAATTACTTAAATTTTTTAAATAAGACGAACAGTCAAACATGTGATAAAAAGTCAACGGCGTCAAACATTTCGAAACTAAGGGAGTAT

Reverse complement sequence

ATACTCCCTTAGTTTCGAAATGTTTGACGCCGTTGACTTTTTATCACATGTTTGACTGTTCGTCTTATTTAAAAAATTTAAGTAATTATTAATTCTTTTT[T/C]
TATCATTTGATTCATTGTTAAATATATTTTTATGTAGGCATATAATTTTACATATCTCACAAAAGTTTTTAAATAAGACGAACGGTTAAACATGTGCTAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.40% 25.50% 0.15% 0.00% NA
All Indica  2759 67.40% 32.30% 0.25% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 1.90% 98.10% 0.00% 0.00% NA
Indica I  595 90.90% 8.70% 0.34% 0.00% NA
Indica II  465 40.60% 58.70% 0.65% 0.00% NA
Indica III  913 65.40% 34.60% 0.00% 0.00% NA
Indica Intermediate  786 67.80% 31.90% 0.25% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0328947114 A -> G LOC_Os03g50690.1 upstream_gene_variant ; 2362.0bp to feature; MODIFIER silent_mutation Average:50.812; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N
vg0328947114 A -> G LOC_Os03g50690-LOC_Os03g50710 intergenic_region ; MODIFIER silent_mutation Average:50.812; most accessible tissue: Zhenshan97 flower, score: 83.061 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0328947114 8.03E-06 4.65E-09 mr1003 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
vg0328947114 NA 1.35E-06 mr1006 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
vg0328947114 NA 1.28E-06 mr1010 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
vg0328947114 8.07E-07 9.60E-10 mr1051 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
vg0328947114 NA 1.37E-06 mr1052 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
vg0328947114 NA 6.98E-07 mr1163 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
vg0328947114 NA 1.40E-09 mr1193 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
vg0328947114 4.28E-06 2.04E-08 mr1536 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
vg0328947114 NA 2.53E-06 mr1671 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
vg0328947114 NA 4.61E-06 mr1931 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
vg0328947114 NA 7.37E-06 mr1974 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
vg0328947114 NA 1.76E-06 mr1952_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