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Detailed information for vg0716080501:

Variant ID: vg0716080501 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16080501
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: 259. )

Flanking Sequence (100 bp) in Reference Genome:


GGGTAGCGCTTCAAGCGTGACTGCTCCTGTTCTTCGTTCTTCGACGACAACGTTGCATCTTCCTCTACTTCTGCTTCACCATGGCTTCTACTGGAGAGAA[C/T]
GGAGGAGACAATATCAATGGAGGCAATACGAATGCCTCAACATCTTCTGCACCATGTACTTTATTTGATTTTCTTCTTGTTATTTACATGTTCACAATGT

Reverse complement sequence

ACATTGTGAACATGTAAATAACAAGAAGAAAATCAAATAAAGTACATGGTGCAGAAGATGTTGAGGCATTCGTATTGCCTCCATTGATATTGTCTCCTCC[G/A]
TTCTCTCCAGTAGAAGCCATGGTGAAGCAGAAGTAGAGGAAGATGCAACGTTGTCGTCGAAGAACGAAGAACAGGAGCAGTCACGCTTGAAGCGCTACCC

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 94.00% 4.60% 0.06% 1.31% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 88.60% 11.40% 0.00% 0.00% NA
Aus  269 75.80% 0.00% 1.12% 23.05% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.50% 0.00% 0.00% NA
Temperate Japonica  767 78.90% 21.10% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 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
vg0716080501 C -> DEL N N silent_mutation Average:19.906; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0716080501 C -> T LOC_Os07g27520.1 upstream_gene_variant ; 2630.0bp to feature; MODIFIER silent_mutation Average:19.906; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0716080501 C -> T LOC_Os07g27510.1 downstream_gene_variant ; 1261.0bp to feature; MODIFIER silent_mutation Average:19.906; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0716080501 C -> T LOC_Os07g27510-LOC_Os07g27520 intergenic_region ; MODIFIER silent_mutation Average:19.906; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716080501 4.14E-15 1.92E-14 mr1265_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
vg0716080501 7.60E-12 3.00E-13 mr1528_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