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Detailed information for vg0217494680:

Variant ID: vg0217494680 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17494680
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: 295. )

Flanking Sequence (100 bp) in Reference Genome:


CAAGCTTTCTCTCTCTTTTGACAACGGACCAAGAGACTCCTCTAAATGCTGCATAATTGAGCAATAACCGATTATACACATGTTGCATCATAGTGCATAA[G/A]
CCCAAGTGTAAGCATGTCATTGATAAAAAAAGCACCCCCAACATTTCCGGGACTCGAAACAATAGCAAGCCAAGTGAACCACAAGCGTTTCCTGGAAAGA

Reverse complement sequence

TCTTTCCAGGAAACGCTTGTGGTTCACTTGGCTTGCTATTGTTTCGAGTCCCGGAAATGTTGGGGGTGCTTTTTTTATCAATGACATGCTTACACTTGGG[C/T]
TTATGCACTATGATGCAACATGTGTATAATCGGTTATTGCTCAATTATGCAGCATTTAGAGGAGTCTCTTGGTCCGTTGTCAAAAGAGAGAGAAAGCTTG

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 67.00% 32.90% 0.08% 0.02% NA
All Indica  2759 50.50% 49.40% 0.14% 0.04% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 73.60% 26.40% 0.00% 0.00% NA
Indica I  595 62.70% 37.00% 0.17% 0.17% NA
Indica II  465 82.80% 16.80% 0.43% 0.00% NA
Indica III  913 22.70% 77.30% 0.00% 0.00% NA
Indica Intermediate  786 54.30% 45.50% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 73.30% 26.70% 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
vg0217494680 G -> A LOC_Os02g29464.1 intron_variant ; MODIFIER silent_mutation Average:41.283; most accessible tissue: Callus, score: 84.458 N N N N
vg0217494680 G -> DEL N N silent_mutation Average:41.283; most accessible tissue: Callus, score: 84.458 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217494680 7.45E-07 6.61E-12 mr1317 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
vg0217494680 2.89E-06 9.47E-07 mr1317 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
vg0217494680 NA 2.27E-08 mr1610 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
vg0217494680 1.47E-07 NA mr1855 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
vg0217494680 1.27E-07 1.40E-08 mr1855 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
vg0217494680 7.19E-06 9.59E-10 mr1927 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
vg0217494680 3.26E-08 4.69E-11 mr1317_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
vg0217494680 3.45E-08 4.46E-08 mr1317_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
vg0217494680 2.83E-06 NA mr1610_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
vg0217494680 7.96E-08 NA mr1818_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
vg0217494680 5.06E-07 2.75E-07 mr1818_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
vg0217494680 6.83E-12 NA mr1855_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
vg0217494680 1.33E-10 1.88E-08 mr1855_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
vg0217494680 1.44E-09 NA mr1897_2 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
vg0217494680 1.16E-08 3.11E-08 mr1897_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
vg0217494680 1.67E-08 NA mr1914_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
vg0217494680 3.75E-08 1.44E-07 mr1914_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
vg0217494680 2.43E-08 NA mr1927_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
vg0217494680 6.45E-07 6.04E-07 mr1927_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