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Detailed information for vg0522637730:

Variant ID: vg0522637730 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22637730
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


CACAAATGGTAGCCCAGTGACCTAAACCACACAGGACTACTACTGAGCAAGTCTGGGAGTGCCCGGCCTCATCTCTGGGCACACTCCAATGTGGACCATG[C/T]
CGGATAAACATTGCTTATGATCAGCTTCTCGTCGTTCGACATGTTAACTTTCTTCTTTAGTAGGTGTGAATCTAGGTAAAATCATGTGCTTTATATGGTT

Reverse complement sequence

AACCATATAAAGCACATGATTTTACCTAGATTCACACCTACTAAAGAAGAAAGTTAACATGTCGAACGACGAGAAGCTGATCATAAGCAATGTTTATCCG[G/A]
CATGGTCCACATTGGAGTGTGCCCAGAGATGAGGCCGGGCACTCCCAGACTTGCTCAGTAGTAGTCCTGTGTGGTTTAGGTCACTGGGCTACCATTTGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.80% 3.80% 0.38% 0.00% NA
All Indica  2759 93.10% 6.40% 0.51% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 97.80% 0.70% 1.49% 0.00% NA
Indica I  595 98.80% 0.70% 0.50% 0.00% NA
Indica II  465 92.50% 6.90% 0.65% 0.00% NA
Indica III  913 89.60% 10.10% 0.33% 0.00% NA
Indica Intermediate  786 93.30% 6.10% 0.64% 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 97.80% 2.20% 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
vg0522637730 C -> T LOC_Os05g38590.1 upstream_gene_variant ; 1606.0bp to feature; MODIFIER silent_mutation Average:66.971; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg0522637730 C -> T LOC_Os05g38590.2 upstream_gene_variant ; 1606.0bp to feature; MODIFIER silent_mutation Average:66.971; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg0522637730 C -> T LOC_Os05g38590.3 upstream_gene_variant ; 1606.0bp to feature; MODIFIER silent_mutation Average:66.971; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg0522637730 C -> T LOC_Os05g38600.1 downstream_gene_variant ; 764.0bp to feature; MODIFIER silent_mutation Average:66.971; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg0522637730 C -> T LOC_Os05g38610.1 downstream_gene_variant ; 3895.0bp to feature; MODIFIER silent_mutation Average:66.971; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N
vg0522637730 C -> T LOC_Os05g38590-LOC_Os05g38600 intergenic_region ; MODIFIER silent_mutation Average:66.971; most accessible tissue: Zhenshan97 panicle, score: 81.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522637730 7.50E-06 1.97E-06 mr1844 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
vg0522637730 NA 4.24E-06 mr1901 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
vg0522637730 NA 1.68E-06 mr1236_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