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Detailed information for vg0821270765:

Variant ID: vg0821270765 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 21270765
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGATAATTTTTTTAAGCCTAATTAATCCATAATTAGAGAATGTTTACTGTAACATCACATAGGCTAATCATGGATTAATTAGGCTCAGTAGATTCGTCT[C/T]
GCGAATTAGTCCAAGATTATGGATGAGTTTTATTAATAGTCTACGTTTAATATTTATAATTAGTGTCCAAACATCCGATGTGATAGGAACTTAAATGTCT

Reverse complement sequence

AGACATTTAAGTTCCTATCACATCGGATGTTTGGACACTAATTATAAATATTAAACGTAGACTATTAATAAAACTCATCCATAATCTTGGACTAATTCGC[G/A]
AGACGAATCTACTGAGCCTAATTAATCCATGATTAGCCTATGTGATGTTACAGTAAACATTCTCTAATTATGGATTAATTAGGCTTAAAAAAATTATCTC

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 90.20% 9.80% 0.00% 0.00% NA
All Indica  2759 95.70% 4.30% 0.00% 0.00% NA
All Japonica  1512 78.20% 21.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 3.90% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 94.50% 5.50% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 4.10% 0.00% 0.00% NA
Temperate Japonica  767 97.50% 2.50% 0.00% 0.00% NA
Tropical Japonica  504 51.60% 48.40% 0.00% 0.00% NA
Japonica Intermediate  241 72.20% 27.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0821270765 C -> T LOC_Os08g33970.1 upstream_gene_variant ; 1875.0bp to feature; MODIFIER silent_mutation Average:51.32; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0821270765 C -> T LOC_Os08g33980.1 upstream_gene_variant ; 2443.0bp to feature; MODIFIER silent_mutation Average:51.32; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0821270765 C -> T LOC_Os08g33960.1 downstream_gene_variant ; 4951.0bp to feature; MODIFIER silent_mutation Average:51.32; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0821270765 C -> T LOC_Os08g33960-LOC_Os08g33970 intergenic_region ; MODIFIER silent_mutation Average:51.32; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0821270765 1.43E-07 NA mr1064_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
vg0821270765 NA 4.31E-06 mr1206_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