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Detailed information for vg0716445309:

Variant ID: vg0716445309 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16445309
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAAACCGGGAAAAAAATCATTTTTAGTCCCGGTTTCTATTCAAACCGGGACTATTATGGTTTTAGCCGATCGGACAAAGATGGTTTCTCCAGTAGTAAC[G/A]
CATATGTATAACTTTATATAAAGTATATACATACAAACATATGTACAAATTTTATGTATACACATGTATAAAAGAATACATGTATACAAACTGCAGTCAC

Reverse complement sequence

GTGACTGCAGTTTGTATACATGTATTCTTTTATACATGTGTATACATAAAATTTGTACATATGTTTGTATGTATATACTTTATATAAAGTTATACATATG[C/T]
GTTACTACTGGAGAAACCATCTTTGTCCGATCGGCTAAAACCATAATAGTCCCGGTTTGAATAGAAACCGGGACTAAAAATGATTTTTTTCCCGGTTTAT

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 80.80% 18.00% 0.00% 1.21% NA
All Indica  2759 77.00% 21.90% 0.00% 1.09% NA
All Japonica  1512 98.10% 0.10% 0.00% 1.79% NA
Aus  269 13.00% 87.00% 0.00% 0.00% NA
Indica I  595 73.10% 26.90% 0.00% 0.00% NA
Indica II  465 87.70% 12.30% 0.00% 0.00% NA
Indica III  913 79.20% 20.70% 0.00% 0.11% NA
Indica Intermediate  786 71.00% 25.30% 0.00% 3.69% NA
Temperate Japonica  767 96.50% 0.00% 0.00% 3.52% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 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
vg0716445309 G -> DEL N N silent_mutation Average:45.446; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0716445309 G -> A LOC_Os07g28170.1 upstream_gene_variant ; 1788.0bp to feature; MODIFIER silent_mutation Average:45.446; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0716445309 G -> A LOC_Os07g28160.1 downstream_gene_variant ; 3168.0bp to feature; MODIFIER silent_mutation Average:45.446; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0716445309 G -> A LOC_Os07g28160-LOC_Os07g28170 intergenic_region ; MODIFIER silent_mutation Average:45.446; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716445309 NA 7.52E-10 mr1222 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
vg0716445309 NA 4.55E-07 mr1510 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
vg0716445309 NA 9.54E-07 mr1847 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
vg0716445309 1.83E-06 NA mr1705_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
vg0716445309 NA 3.17E-08 mr1705_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