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Detailed information for vg0205808842:

Variant ID: vg0205808842 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5808842
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTATTTGTTTCTTTCCTTTTTTATCAATTCAAATTTGAATTTGGATGAAACTCCTCGAAATCTCAAACAGTTTATACTTTCAAGCCTCGTCGGAATGTC[G/A]
AAATTTCGCAAAATCCGACCGGATTTCGTTGGAATTGTAAACCCTGAATGCAACTATGTCACATCATCACCCACTAGCAATAGTTACATATTTAACCTTA

Reverse complement sequence

TAAGGTTAAATATGTAACTATTGCTAGTGGGTGATGATGTGACATAGTTGCATTCAGGGTTTACAATTCCAACGAAATCCGGTCGGATTTTGCGAAATTT[C/T]
GACATTCCGACGAGGCTTGAAAGTATAAACTGTTTGAGATTTCGAGGAGTTTCATCCAAATTCAAATTTGAATTGATAAAAAAGGAAAGAAACAAATAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.50% 2.50% 0.00% 0.00% NA
All Indica  2759 95.80% 4.20% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 93.00% 7.00% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0205808842 G -> A LOC_Os02g10920.4 upstream_gene_variant ; 2447.0bp to feature; MODIFIER silent_mutation Average:36.399; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0205808842 G -> A LOC_Os02g10920.5 upstream_gene_variant ; 2447.0bp to feature; MODIFIER silent_mutation Average:36.399; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0205808842 G -> A LOC_Os02g10920.6 upstream_gene_variant ; 2341.0bp to feature; MODIFIER silent_mutation Average:36.399; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0205808842 G -> A LOC_Os02g10930.1 downstream_gene_variant ; 1888.0bp to feature; MODIFIER silent_mutation Average:36.399; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0205808842 G -> A LOC_Os02g10940.1 downstream_gene_variant ; 3252.0bp to feature; MODIFIER silent_mutation Average:36.399; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0205808842 G -> A LOC_Os02g10930-LOC_Os02g10940 intergenic_region ; MODIFIER silent_mutation Average:36.399; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205808842 8.19E-06 5.08E-08 mr1676_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
vg0205808842 NA 8.89E-08 mr1798_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
vg0205808842 NA 2.54E-06 mr1970_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
vg0205808842 NA 4.41E-07 mr1973_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