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Detailed information for vg0720602295:

Variant ID: vg0720602295 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20602295
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATTCAGAGAGTACAATGCAGGCATCAACTTCGGGCCTATTTGGTAGAGTTCCAACTCCTAAATTTAGCTACAGGAGTTGAGTCTGCAGTGGAGTTGTG[G/A]
AGCTGCCTGAACCTAGCTTCACCTCTCTAGTTTATTTTATGAGAGAGATCCATCTAGCTCCACTTACATTTTAAGTGGAGCTGAAACTGTTTGGATGAGC

Reverse complement sequence

GCTCATCCAAACAGTTTCAGCTCCACTTAAAATGTAAGTGGAGCTAGATGGATCTCTCTCATAAAATAAACTAGAGAGGTGAAGCTAGGTTCAGGCAGCT[C/T]
CACAACTCCACTGCAGACTCAACTCCTGTAGCTAAATTTAGGAGTTGGAACTCTACCAAATAGGCCCGAAGTTGATGCCTGCATTGTACTCTCTGAATGA

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 89.10% 10.60% 0.06% 0.25% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 66.70% 32.30% 0.20% 0.79% 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 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 69.90% 28.30% 0.26% 1.56% NA
Tropical Japonica  504 73.80% 26.20% 0.00% 0.00% NA
Japonica Intermediate  241 41.90% 57.70% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0720602295 G -> DEL N N silent_mutation Average:62.535; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0720602295 G -> A LOC_Os07g34370.1 upstream_gene_variant ; 2091.0bp to feature; MODIFIER silent_mutation Average:62.535; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0720602295 G -> A LOC_Os07g34380.1 downstream_gene_variant ; 366.0bp to feature; MODIFIER silent_mutation Average:62.535; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N
vg0720602295 G -> A LOC_Os07g34370-LOC_Os07g34380 intergenic_region ; MODIFIER silent_mutation Average:62.535; most accessible tissue: Minghui63 panicle, score: 88.281 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720602295 NA 1.76E-10 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0720602295 NA 4.04E-06 mr1183 Jap_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
vg0720602295 NA 6.02E-07 mr1548_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
vg0720602295 NA 2.79E-06 mr1561_2 Jap_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
vg0720602295 NA 2.56E-06 mr1836_2 Jap_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
vg0720602295 2.31E-06 2.31E-06 mr1908_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