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Detailed information for vg0609019806:

Variant ID: vg0609019806 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9019806
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


ACCCCAACGTGGTCGACGTAATGCCGAGCAAGGTCACCAAGGTGCTCAAACCGGACACGGCGCTTGCCATTGTTGACGGTCATTAGCGATCAGTTTCGAC[C/T]
GTCAATATTACCATAATAGAGGAGAACTAGTTATGCTTGCAATGCATATTCATGTTAGGATAATAATATTCCACTAGTGTTTGGTTCACTAACCTTTTGC

Reverse complement sequence

GCAAAAGGTTAGTGAACCAAACACTAGTGGAATATTATTATCCTAACATGAATATGCATTGCAAGCATAACTAGTTCTCCTCTATTATGGTAATATTGAC[G/A]
GTCGAAACTGATCGCTAATGACCGTCAACAATGGCAAGCGCCGTGTCCGGTTTGAGCACCTTGGTGACCTTGCTCGGCATTACGTCGACCACGTTGGGGT

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 93.40% 6.60% 0.00% 0.00% NA
All Indica  2759 97.40% 2.60% 0.00% 0.00% NA
All Japonica  1512 90.30% 9.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 92.10% 7.90% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 96.60% 3.40% 0.00% 0.00% NA
Tropical Japonica  504 87.10% 12.90% 0.00% 0.00% NA
Japonica Intermediate  241 76.80% 23.20% 0.00% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0609019806 C -> T LOC_Os06g15890.1 upstream_gene_variant ; 18.0bp to feature; MODIFIER silent_mutation Average:52.974; most accessible tissue: Zhenshan97 young leaf, score: 67.83 N N N N
vg0609019806 C -> T LOC_Os06g15900.1 upstream_gene_variant ; 1608.0bp to feature; MODIFIER silent_mutation Average:52.974; most accessible tissue: Zhenshan97 young leaf, score: 67.83 N N N N
vg0609019806 C -> T LOC_Os06g15880.1 downstream_gene_variant ; 1170.0bp to feature; MODIFIER silent_mutation Average:52.974; most accessible tissue: Zhenshan97 young leaf, score: 67.83 N N N N
vg0609019806 C -> T LOC_Os06g15890-LOC_Os06g15900 intergenic_region ; MODIFIER silent_mutation Average:52.974; most accessible tissue: Zhenshan97 young leaf, score: 67.83 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609019806 3.81E-07 2.65E-16 mr1842 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
vg0609019806 NA 6.33E-10 mr1829_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
vg0609019806 2.99E-06 1.38E-17 mr1842_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