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Detailed information for vg0720600655:

Variant ID: vg0720600655 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20600655
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGTATAAACTTTGTATACACATATACAAAGTTTATATGTATATATATATATACACACACACACGTATGCATATTGTATATATGTATATTTTTAAAATTT[G/A]
TATATATTTTTTATATACAAAGTTTGTATATGTATACATACAAAATATACCAATTTTATATACGCATAAATCCAAAGTTTATATATGTATACCTACAAAA

Reverse complement sequence

TTTTGTAGGTATACATATATAAACTTTGGATTTATGCGTATATAAAATTGGTATATTTTGTATGTATACATATACAAACTTTGTATATAAAAAATATATA[C/T]
AAATTTTAAAAATATACATATATACAATATGCATACGTGTGTGTGTGTATATATATATATACATATAAACTTTGTATATGTGTATACAAAGTTTATACGT

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 91.70% 7.90% 0.17% 0.25% NA
All Indica  2759 86.80% 12.90% 0.25% 0.00% NA
All Japonica  1512 98.80% 0.30% 0.07% 0.79% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.10% 7.90% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 80.10% 19.80% 0.11% 0.00% NA
Indica Intermediate  786 84.20% 15.00% 0.76% 0.00% NA
Temperate Japonica  767 98.30% 0.10% 0.00% 1.56% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0720600655 G -> DEL N N silent_mutation Average:46.718; most accessible tissue: Minghui63 panicle, score: 91.756 N N N N
vg0720600655 G -> A LOC_Os07g34370.1 upstream_gene_variant ; 451.0bp to feature; MODIFIER silent_mutation Average:46.718; most accessible tissue: Minghui63 panicle, score: 91.756 N N N N
vg0720600655 G -> A LOC_Os07g34380.1 downstream_gene_variant ; 2006.0bp to feature; MODIFIER silent_mutation Average:46.718; most accessible tissue: Minghui63 panicle, score: 91.756 N N N N
vg0720600655 G -> A LOC_Os07g34370-LOC_Os07g34380 intergenic_region ; MODIFIER silent_mutation Average:46.718; most accessible tissue: Minghui63 panicle, score: 91.756 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720600655 1.48E-06 1.31E-06 mr1367 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
vg0720600655 8.49E-07 8.49E-07 mr1367 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
vg0720600655 NA 6.97E-06 mr1795 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