Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0521133620:

Variant ID: vg0521133620 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 21133620
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TAATTACACAGTAATATTTTTAAAATGTGATGTACCATGAATACACGCTTGTTTTTTTATATATAAGATAGATCTAATGGTTAGAAATAATGGTTTCACA[G/T]
ATTTAAAAAGCATAGGAGTATTCCATATATGTAGCTTATGGTTGCTTTAATTATGTAGTTGGTGACTTACGAACACTCTTGAGGGCATTTAATTGATTTT

Reverse complement sequence

AAAATCAATTAAATGCCCTCAAGAGTGTTCGTAAGTCACCAACTACATAATTAAAGCAACCATAAGCTACATATATGGAATACTCCTATGCTTTTTAAAT[C/A]
TGTGAAACCATTATTTCTAACCATTAGATCTATCTTATATATAAAAAAACAAGCGTGTATTCATGGTACATCACATTTTAAAAATATTACTGTGTAATTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.60% 1.20% 0.19% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.10% 3.50% 0.40% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.20% 0.39% 0.00% NA
Tropical Japonica  504 91.10% 8.50% 0.40% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 2.22% 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
vg0521133620 G -> T LOC_Os05g35540.1 upstream_gene_variant ; 3975.0bp to feature; MODIFIER silent_mutation Average:28.687; most accessible tissue: Zhenshan97 root, score: 43.05 N N N N
vg0521133620 G -> T LOC_Os05g35560.1 upstream_gene_variant ; 1163.0bp to feature; MODIFIER silent_mutation Average:28.687; most accessible tissue: Zhenshan97 root, score: 43.05 N N N N
vg0521133620 G -> T LOC_Os05g35550.1 downstream_gene_variant ; 3432.0bp to feature; MODIFIER silent_mutation Average:28.687; most accessible tissue: Zhenshan97 root, score: 43.05 N N N N
vg0521133620 G -> T LOC_Os05g35570.1 downstream_gene_variant ; 1618.0bp to feature; MODIFIER silent_mutation Average:28.687; most accessible tissue: Zhenshan97 root, score: 43.05 N N N N
vg0521133620 G -> T LOC_Os05g35560-LOC_Os05g35570 intergenic_region ; MODIFIER silent_mutation Average:28.687; most accessible tissue: Zhenshan97 root, score: 43.05 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0521133620 5.84E-07 1.15E-06 mr1104 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
vg0521133620 8.22E-06 NA mr1155 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
vg0521133620 1.43E-06 1.43E-06 mr1076_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