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Detailed information for vg0823443665:

Variant ID: vg0823443665 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 23443665
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTGACGAAAACCACCGCCACCGTCCACCAAGGTTTCAAAAGAGAGAAGACTAGGCTTTCGCCCGGCAACCACCCTTGAGGGGTGAGACGGCACGACAAC[G/A]
CCCTTAGGAGGGGGAATGACACTCGAGCTCTATCGTTGTCGGTCCGGCCAAGGCCGGGTTGGGTTTTCACCTGCCGCTCACCACTTGCGAGTCCACGGCT

Reverse complement sequence

AGCCGTGGACTCGCAAGTGGTGAGCGGCAGGTGAAAACCCAACCCGGCCTTGGCCGGACCGACAACGATAGAGCTCGAGTGTCATTCCCCCTCCTAAGGG[C/T]
GTTGTCGTGCCGTCTCACCCCTCAAGGGTGGTTGCCGGGCGAAAGCCTAGTCTTCTCTCTTTTGAAACCTTGGTGGACGGTGGCGGTGGTTTTCGTCACT

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 96.20% 3.40% 0.40% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 88.60% 10.20% 1.26% 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 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 0.10% 0.91% 0.00% NA
Tropical Japonica  504 69.20% 28.60% 2.18% 0.00% NA
Japonica Intermediate  241 95.90% 3.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0823443665 G -> A LOC_Os08g37104.1 upstream_gene_variant ; 3947.0bp to feature; MODIFIER silent_mutation Average:67.272; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N
vg0823443665 G -> A LOC_Os08g37080.1 downstream_gene_variant ; 2145.0bp to feature; MODIFIER silent_mutation Average:67.272; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N
vg0823443665 G -> A LOC_Os08g37090.1 downstream_gene_variant ; 477.0bp to feature; MODIFIER silent_mutation Average:67.272; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N
vg0823443665 G -> A LOC_Os08g37080-LOC_Os08g37090 intergenic_region ; MODIFIER silent_mutation Average:67.272; most accessible tissue: Zhenshan97 panicle, score: 81.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0823443665 8.25E-06 8.25E-06 mr1131 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
vg0823443665 NA 7.52E-06 mr1006_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
vg0823443665 NA 4.41E-07 mr1068_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
vg0823443665 NA 3.26E-07 mr1090_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
vg0823443665 NA 9.35E-06 mr1094_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
vg0823443665 NA 6.32E-07 mr1096_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
vg0823443665 NA 2.69E-06 mr1112_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
vg0823443665 NA 1.78E-06 mr1121_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
vg0823443665 8.60E-06 1.46E-07 mr1200_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
vg0823443665 NA 2.53E-06 mr1211_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
vg0823443665 2.05E-06 2.05E-06 mr1234_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
vg0823443665 NA 6.82E-06 mr1786_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
vg0823443665 NA 4.37E-07 mr1896_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