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Detailed information for vg1217635882:

Variant ID: vg1217635882 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17635882
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAAGTGCAGTTATGGAAATCCGTGTCCAACGTTTGACCGTCCGCCTTATTTGAAAAATTTATAATTTTTTTAAAAAATAGTCACACATAAAGTACTCTT[C/T]
GTGTTTTATCATCTAACAACAATAAAAAATACTAATCATAAAAAATTTCAAATAAGATAAACGGTGAAACGTTGGATATTAATAGTACAAAACTATACTT

Reverse complement sequence

AAGTATAGTTTTGTACTATTAATATCCAACGTTTCACCGTTTATCTTATTTGAAATTTTTTATGATTAGTATTTTTTATTGTTGTTAGATGATAAAACAC[G/A]
AAGAGTACTTTATGTGTGACTATTTTTTAAAAAAATTATAAATTTTTCAAATAAGGCGGACGGTCAAACGTTGGACACGGATTTCCATAACTGCACTTAT

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 95.70% 4.30% 0.00% 0.00% NA
All Indica  2759 95.10% 4.90% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 75.50% 24.50% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 81.90% 18.10% 0.00% 0.00% NA
Indica III  913 97.90% 2.10% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 4.10% 0.00% 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 99.20% 0.80% 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
vg1217635882 C -> T LOC_Os12g29580.1 upstream_gene_variant ; 3456.0bp to feature; MODIFIER silent_mutation Average:55.221; most accessible tissue: Zhenshan97 panicle, score: 92.403 N N N N
vg1217635882 C -> T LOC_Os12g29580.2 upstream_gene_variant ; 3490.0bp to feature; MODIFIER silent_mutation Average:55.221; most accessible tissue: Zhenshan97 panicle, score: 92.403 N N N N
vg1217635882 C -> T LOC_Os12g29580-LOC_Os12g29590 intergenic_region ; MODIFIER silent_mutation Average:55.221; most accessible tissue: Zhenshan97 panicle, score: 92.403 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217635882 NA 1.86E-06 mr1188 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
vg1217635882 7.88E-07 2.49E-07 mr1268 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
vg1217635882 NA 3.26E-06 mr1268 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
vg1217635882 NA 1.35E-06 mr1188_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