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Detailed information for vg0820509533:

Variant ID: vg0820509533 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20509533
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TACAACCGTCGCTCACATCAAGATCAAATGTTGTGGAATCCAATTCGGTCACCTGCTATACTGTTGACTTCAATTGGCCGTCAAAGTTGCATACGAGCTC[C/T]
GTTTTTTGGTCCATGAGTACTTGATGGAAAGCTCTTGGAATCCTCTTTCCAATAGATACAGCCTCATTACTAAATTCCATCCCAGTCATCCACAATCACA

Reverse complement sequence

TGTGATTGTGGATGACTGGGATGGAATTTAGTAATGAGGCTGTATCTATTGGAAAGAGGATTCCAAGAGCTTTCCATCAAGTACTCATGGACCAAAAAAC[G/A]
GAGCTCGTATGCAACTTTGACGGCCAATTGAAGTCAACAGTATAGCAGGTGACCGAATTGGATTCCACAACATTTGATCTTGATGTGAGCGACGGTTGTA

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 98.10% 1.20% 0.68% 0.00% NA
All Indica  2759 98.80% 1.20% 0.04% 0.00% NA
All Japonica  1512 96.40% 1.70% 1.98% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 96.90% 3.00% 0.11% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 94.70% 2.50% 2.87% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 95.00% 2.50% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0820509533 C -> T LOC_Os08g33040.1 upstream_gene_variant ; 2431.0bp to feature; MODIFIER silent_mutation Average:55.614; most accessible tissue: Zhenshan97 young leaf, score: 73.54 N N N N
vg0820509533 C -> T LOC_Os08g33030-LOC_Os08g33040 intergenic_region ; MODIFIER silent_mutation Average:55.614; most accessible tissue: Zhenshan97 young leaf, score: 73.54 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820509533 NA 2.27E-07 mr1851 Jap_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
vg0820509533 2.20E-06 2.20E-06 mr1004_2 Jap_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
vg0820509533 NA 8.51E-07 mr1510_2 Jap_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
vg0820509533 8.53E-06 1.98E-08 mr1531_2 Jap_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
vg0820509533 NA 8.55E-07 mr1702_2 Jap_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
vg0820509533 NA 1.61E-07 mr1788_2 Jap_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