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Detailed information for vg0321868776:

Variant ID: vg0321868776 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21868776
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: 104. )

Flanking Sequence (100 bp) in Reference Genome:


AGCAGCCTCTGCAACCGATCCAACAGACTACGTTAAGGCAGCAAATCATTCAGCCGATTCAGCAACAGGGGTCTGTAAGCGCATCGGCCGGGTTCGCAGC[G/A]
CCTAGAGGTCAGCCTATACAACAATTTGTAAACCAAGTCATCCCAGAACATTTGGTTCACCACGTACAGCCGGACGGCACAGTAATGCCTTAGGTTGTTC

Reverse complement sequence

GAACAACCTAAGGCATTACTGTGCCGTCCGGCTGTACGTGGTGAACCAAATGTTCTGGGATGACTTGGTTTACAAATTGTTGTATAGGCTGACCTCTAGG[C/T]
GCTGCGAACCCGGCCGATGCGCTTACAGACCCCTGTTGCTGAATCGGCTGAATGATTTGCTGCCTTAACGTAGTCTGTTGGATCGGTTGCAGAGGCTGCT

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 47.40% 18.70% 4.42% 29.50% NA
All Indica  2759 20.40% 29.50% 3.70% 46.39% NA
All Japonica  1512 98.30% 0.10% 0.00% 1.59% NA
Aus  269 12.30% 23.00% 38.29% 26.39% NA
Indica I  595 25.90% 58.00% 2.18% 13.95% NA
Indica II  465 29.50% 12.00% 2.37% 56.13% NA
Indica III  913 4.10% 29.70% 4.82% 61.45% NA
Indica Intermediate  786 30.00% 17.90% 4.33% 47.71% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 95.40% 0.00% 0.00% 4.56% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 96.90% 0.00% 1.04% 2.08% NA
Intermediate  90 68.90% 8.90% 3.33% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0321868776 G -> A LOC_Os03g39350.1 intron_variant ; MODIFIER silent_mutation Average:66.325; most accessible tissue: Minghui63 young leaf, score: 79.191 N N N N
vg0321868776 G -> DEL N N silent_mutation Average:66.325; most accessible tissue: Minghui63 young leaf, score: 79.191 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321868776 NA 1.61E-20 mr1689 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
vg0321868776 3.76E-06 NA mr1718 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
vg0321868776 3.26E-06 2.46E-09 mr1718 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
vg0321868776 7.65E-07 NA mr1750 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
vg0321868776 4.84E-06 1.62E-11 mr1750 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
vg0321868776 NA 2.06E-16 mr1842 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
vg0321868776 NA 2.76E-07 mr1850 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
vg0321868776 NA 8.28E-07 mr1568_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
vg0321868776 1.27E-08 NA mr1718_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
vg0321868776 2.03E-08 4.69E-10 mr1718_2 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