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Detailed information for vg0805470240:

Variant ID: vg0805470240 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5470240
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTAAAAATTAAAAAGGTTTAAAAAATTTAAAAAAAAAATCGATGTCCAGTGCCTTGCTCGTGCGTGCAATCCGATGCCATCAAGGCATCGAAACCAAC[G/A]
TCTCCATTAATTCTCGCATCACAAGAAGCAATGCTCTATCTACAACTAGGCATGGTCAACCAAATTGCAACATGAGAATCGTTGGGGAAAGAAAAATGCT

Reverse complement sequence

AGCATTTTTCTTTCCCCAACGATTCTCATGTTGCAATTTGGTTGACCATGCCTAGTTGTAGATAGAGCATTGCTTCTTGTGATGCGAGAATTAATGGAGA[C/T]
GTTGGTTTCGATGCCTTGATGGCATCGGATTGCACGCACGAGCAAGGCACTGGACATCGATTTTTTTTTTAAATTTTTTAAACCTTTTTAATTTTTAAAA

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 97.90% 1.40% 0.72% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 93.40% 4.40% 2.25% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 88.10% 7.80% 4.04% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 1.20% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0805470240 G -> A LOC_Os08g09430.1 upstream_gene_variant ; 936.0bp to feature; MODIFIER silent_mutation Average:59.025; most accessible tissue: Callus, score: 84.941 N N N N
vg0805470240 G -> A LOC_Os08g09440.1 upstream_gene_variant ; 386.0bp to feature; MODIFIER silent_mutation Average:59.025; most accessible tissue: Callus, score: 84.941 N N N N
vg0805470240 G -> A LOC_Os08g09450.1 downstream_gene_variant ; 4755.0bp to feature; MODIFIER silent_mutation Average:59.025; most accessible tissue: Callus, score: 84.941 N N N N
vg0805470240 G -> A LOC_Os08g09430-LOC_Os08g09440 intergenic_region ; MODIFIER silent_mutation Average:59.025; most accessible tissue: Callus, score: 84.941 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805470240 7.02E-07 4.79E-06 mr1330_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