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Detailed information for vg0805195004:

Variant ID: vg0805195004 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5195004
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


AGAAAAAAATAGGTTGACGCCATGAAATTGATTTTGTAGTAGTGAGAAAGAAGAGTTTGACCTAGATGAAGCAGTTCTGAGAGCAGTCACGCAAAGAACA[C/T]
GCTCTCTAAAAACTTGATCGCCCGTCTATCCAAGTAGTCAGATGGACGGATTTCCGGAAGCCTGCTCGTTACAAACACTCGTGCGCGCAGGTAATCTATT

Reverse complement sequence

AATAGATTACCTGCGCGCACGAGTGTTTGTAACGAGCAGGCTTCCGGAAATCCGTCCATCTGACTACTTGGATAGACGGGCGATCAAGTTTTTAGAGAGC[G/A]
TGTTCTTTGCGTGACTGCTCTCAGAACTGCTTCATCTAGGTCAAACTCTTCTTTCTCACTACTACAAAATCAATTTCATGGCGTCAACCTATTTTTTTCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.20% 43.80% 0.00% 0.00% NA
All Indica  2759 81.40% 18.60% 0.00% 0.00% NA
All Japonica  1512 1.40% 98.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 93.30% 6.70% 0.00% 0.00% NA
Indica II  465 40.40% 59.60% 0.00% 0.00% NA
Indica III  913 92.20% 7.80% 0.00% 0.00% NA
Indica Intermediate  786 84.20% 15.80% 0.00% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 2.40% 97.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.90% 97.10% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 47.80% 52.20% 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
vg0805195004 C -> T LOC_Os08g08940.1 upstream_gene_variant ; 1107.0bp to feature; MODIFIER silent_mutation Average:63.644; most accessible tissue: Zhenshan97 flower, score: 79.53 N N N N
vg0805195004 C -> T LOC_Os08g08930.1 downstream_gene_variant ; 699.0bp to feature; MODIFIER silent_mutation Average:63.644; most accessible tissue: Zhenshan97 flower, score: 79.53 N N N N
vg0805195004 C -> T LOC_Os08g08930-LOC_Os08g08940 intergenic_region ; MODIFIER silent_mutation Average:63.644; most accessible tissue: Zhenshan97 flower, score: 79.53 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805195004 NA 2.29E-06 mr1358_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
vg0805195004 NA 7.12E-06 mr1580_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
vg0805195004 NA 2.39E-06 mr1732_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
vg0805195004 NA 8.87E-19 mr1874_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
vg0805195004 NA 7.29E-14 mr1893_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
vg0805195004 NA 5.66E-06 mr1893_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