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Detailed information for vg0619574951:

Variant ID: vg0619574951 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19574951
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: 327. )

Flanking Sequence (100 bp) in Reference Genome:


ACATAGGGGTGAGACCACCCGCTTACTAGTCCAGTGCCATGGCATCTCGACTAACGGACACCGGCCCGTGTAGCCTTCATTTGCCTAGACATCTCGATTA[C/T]
CGAGCCGCAGCTCGCATAGCCTTCATTTGCCTCAGAGATATCCATCGTCGCAACGACTTCATCCATCTCTCTCCGTGTCCTTTTGTTCAGGACTAGGCTG

Reverse complement sequence

CAGCCTAGTCCTGAACAAAAGGACACGGAGAGAGATGGATGAAGTCGTTGCGACGATGGATATCTCTGAGGCAAATGAAGGCTATGCGAGCTGCGGCTCG[G/A]
TAATCGAGATGTCTAGGCAAATGAAGGCTACACGGGCCGGTGTCCGTTAGTCGAGATGCCATGGCACTGGACTAGTAAGCGGGTGGTCTCACCCCTATGT

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 94.70% 5.20% 0.02% 0.00% NA
All Indica  2759 99.30% 0.70% 0.04% 0.00% NA
All Japonica  1512 84.90% 15.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.00% 1.80% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 74.40% 25.60% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 87.60% 12.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0619574951 C -> T LOC_Os06g33620.1 upstream_gene_variant ; 1681.0bp to feature; MODIFIER silent_mutation Average:56.66; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0619574951 C -> T LOC_Os06g33630.1 downstream_gene_variant ; 3908.0bp to feature; MODIFIER silent_mutation Average:56.66; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0619574951 C -> T LOC_Os06g33610-LOC_Os06g33620 intergenic_region ; MODIFIER silent_mutation Average:56.66; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619574951 NA 2.37E-07 mr1062_2 Jap_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
vg0619574951 NA 6.21E-06 mr1456_2 Jap_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
vg0619574951 NA 1.87E-06 mr1565_2 Jap_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
vg0619574951 2.51E-06 2.51E-06 mr1914_2 Jap_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
vg0619574951 NA 5.44E-07 mr1915_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
vg0619574951 7.15E-06 NA mr1923_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