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Detailed information for vg0102728977:

Variant ID: vg0102728977 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2728977
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TTAATCTGGATTGTAGAGCATACTGATATGTTCAATGCCTAGATGACAAAACTTCAACATGGGCTACCGCATTCTATTATTATTATTTTTAAAATTGTAC[T/A]
ACAAAAGAAAGGGACTAAAAAGGATTTCTGATTGAGCCTAAAAGGCTAATTACCATCTGGTAGCTCTTCATTGTTAGGCGGCCTAAGGTTTACTACCTTG

Reverse complement sequence

CAAGGTAGTAAACCTTAGGCCGCCTAACAATGAAGAGCTACCAGATGGTAATTAGCCTTTTAGGCTCAATCAGAAATCCTTTTTAGTCCCTTTCTTTTGT[A/T]
GTACAATTTTAAAAATAATAATAATAGAATGCGGTAGCCCATGTTGAAGTTTTGTCATCTAGGCATTGAACATATCAGTATGCTCTACAATCCAGATTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.30% 12.70% 0.02% 0.00% NA
All Indica  2759 79.30% 20.60% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 97.10% 2.90% 0.00% 0.00% NA
Indica II  465 69.50% 30.50% 0.00% 0.00% NA
Indica III  913 74.50% 25.40% 0.11% 0.00% NA
Indica Intermediate  786 77.40% 22.60% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 78.90% 21.10% 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
vg0102728977 T -> A LOC_Os01g05710.1 downstream_gene_variant ; 4180.0bp to feature; MODIFIER silent_mutation Average:49.958; most accessible tissue: Callus, score: 69.853 N N N N
vg0102728977 T -> A LOC_Os01g05720.1 intron_variant ; MODIFIER silent_mutation Average:49.958; most accessible tissue: Callus, score: 69.853 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102728977 NA 3.70E-08 mr1498 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
vg0102728977 NA 1.75E-08 mr1498_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
vg0102728977 NA 3.03E-07 mr1498_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
vg0102728977 4.16E-07 5.91E-09 mr1769_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
vg0102728977 NA 1.02E-07 mr1951_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
vg0102728977 3.23E-07 6.58E-10 mr1951_2 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