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Detailed information for vg0221479912:

Variant ID: vg0221479912 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21479912
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TCAAGGTCTTAATCAATGTTCATCATTGCCTAAATATAAAAGTTCAACAATATTCATTATTTTAGTTTAAGCCTAAACATTCCTTTGGGGTTAATTATTT[C/T]
GCGGAGGATGAAGCCGGCTATCTCCTCACGAATCTCCTCAAAGTTGGTAGGCAGAGACTTGGTAATTTTGCCCTACATTGTCATAATTCAAGATTAGTTG

Reverse complement sequence

CAACTAATCTTGAATTATGACAATGTAGGGCAAAATTACCAAGTCTCTGCCTACCAACTTTGAGGAGATTCGTGAGGAGATAGCCGGCTTCATCCTCCGC[G/A]
AAATAATTAACCCCAAAGGAATGTTTAGGCTTAAACTAAAATAATGAATATTGTTGAACTTTTATATTTAGGCAATGATGAACATTGATTAAGACCTTGA

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 97.30% 1.40% 1.29% 0.00% NA
All Indica  2759 95.30% 2.50% 2.21% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.10% 0.80% 4.03% 0.00% NA
Indica II  465 98.70% 1.10% 0.22% 0.00% NA
Indica III  913 98.60% 1.20% 0.22% 0.00% NA
Indica Intermediate  786 89.70% 6.00% 4.33% 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  90 100.00% 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
vg0221479912 C -> T LOC_Os02g35760.1 upstream_gene_variant ; 2280.0bp to feature; MODIFIER silent_mutation Average:41.954; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0221479912 C -> T LOC_Os02g35760.2 upstream_gene_variant ; 2280.0bp to feature; MODIFIER silent_mutation Average:41.954; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0221479912 C -> T LOC_Os02g35750.2 downstream_gene_variant ; 4444.0bp to feature; MODIFIER silent_mutation Average:41.954; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0221479912 C -> T LOC_Os02g35750.3 downstream_gene_variant ; 4279.0bp to feature; MODIFIER silent_mutation Average:41.954; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0221479912 C -> T LOC_Os02g35760-LOC_Os02g35770 intergenic_region ; MODIFIER silent_mutation Average:41.954; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221479912 5.53E-07 5.53E-07 mr1449 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
vg0221479912 NA 8.41E-06 mr1533 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
vg0221479912 NA 3.60E-07 mr1980 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
vg0221479912 NA 6.67E-09 mr1533_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
vg0221479912 NA 2.27E-07 mr1980_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