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Detailed information for vg0221483879:

Variant ID: vg0221483879 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21483879
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: 124. )

Flanking Sequence (100 bp) in Reference Genome:


TGTAAAAACGTGCAACACTCTGTGTTCGTTTCTCCAACAAGACATGGATTAAATTTTAGATACTCGTGGCATATTTTTCAAACTACTAAACTGTGCGTTT[C/T]
GTGCAAGAACTTTATATATGAAAGTTGCTCTAAAATATCAGTTTAATCTATTTTTCAAGTTTGTAATAATTAAAACTCAATTAATCACATATTATTACCA

Reverse complement sequence

TGGTAATAATATGTGATTAATTGAGTTTTAATTATTACAAACTTGAAAAATAGATTAAACTGATATTTTAGAGCAACTTTCATATATAAAGTTCTTGCAC[G/A]
AAACGCACAGTTTAGTAGTTTGAAAAATATGCCACGAGTATCTAAAATTTAATCCATGTCTTGTTGGAGAAACGAACACAGAGTGTTGCACGTTTTTACA

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 94.20% 4.70% 1.12% 0.00% NA
All Indica  2759 90.20% 7.90% 1.88% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 0.00% 1.85% 0.00% NA
Indica II  465 78.10% 17.00% 4.95% 0.00% NA
Indica III  913 94.30% 5.60% 0.11% 0.00% NA
Indica Intermediate  786 86.60% 11.20% 2.16% 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 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0221483879 C -> T LOC_Os02g35770.1 downstream_gene_variant ; 3716.0bp to feature; MODIFIER silent_mutation Average:49.547; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0221483879 C -> T LOC_Os02g35770.2 downstream_gene_variant ; 3716.0bp to feature; MODIFIER silent_mutation Average:49.547; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N
vg0221483879 C -> T LOC_Os02g35760-LOC_Os02g35770 intergenic_region ; MODIFIER silent_mutation Average:49.547; most accessible tissue: Minghui63 panicle, score: 74.563 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221483879 NA 2.60E-06 mr1098 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
vg0221483879 NA 2.55E-06 mr1150 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
vg0221483879 NA 2.81E-07 mr1589 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
vg0221483879 3.55E-06 NA mr1918 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
vg0221483879 4.40E-06 1.62E-07 mr1918 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