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Detailed information for vg0820710287:

Variant ID: vg0820710287 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 20710287
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAGGGACTCGGGTTAAATTCCAAACTTGTATGTCAAGGAAATACCCGGGATCCTAGTTGGTTACGATTGTATTTTGTATGTAACTACCTATTCCATTAG[A/G]
GATATGGACTGTACTTAGGAGGGGTCCGGGTGCCTCTTGGGGCACGATTTTGCTCCTAGATCATACGATCAATAATACACTCGGCGGATCAATCCCCGGA

Reverse complement sequence

TCCGGGGATTGATCCGCCGAGTGTATTATTGATCGTATGATCTAGGAGCAAAATCGTGCCCCAAGAGGCACCCGGACCCCTCCTAAGTACAGTCCATATC[T/C]
CTAATGGAATAGGTAGTTACATACAAAATACAATCGTAACCAACTAGGATCCCGGGTATTTCCTTGACATACAAGTTTGGAATTTAACCCGAGTCCCTTT

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 83.40% 15.30% 1.25% 0.00% NA
All Indica  2759 99.60% 0.30% 0.04% 0.00% NA
All Japonica  1512 50.20% 46.30% 3.51% 0.00% NA
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.80% 0.13% 0.00% NA
Temperate Japonica  767 24.50% 70.40% 5.08% 0.00% NA
Tropical Japonica  504 89.30% 9.10% 1.59% 0.00% NA
Japonica Intermediate  241 50.20% 47.30% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 80.00% 16.70% 3.33% 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
vg0820710287 A -> G LOC_Os08g33220.1 upstream_gene_variant ; 277.0bp to feature; MODIFIER silent_mutation Average:63.469; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0820710287 A -> G LOC_Os08g33230.1 upstream_gene_variant ; 3168.0bp to feature; MODIFIER silent_mutation Average:63.469; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0820710287 A -> G LOC_Os08g33240.1 downstream_gene_variant ; 4582.0bp to feature; MODIFIER silent_mutation Average:63.469; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0820710287 A -> G LOC_Os08g33210-LOC_Os08g33220 intergenic_region ; MODIFIER silent_mutation Average:63.469; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820710287 NA 2.29E-06 mr1124 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
vg0820710287 1.04E-06 NA mr1388 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
vg0820710287 6.73E-06 2.24E-07 mr1388 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
vg0820710287 NA 8.46E-08 mr1227_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
vg0820710287 NA 4.88E-10 mr1282_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
vg0820710287 NA 1.30E-10 mr1993_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