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Detailed information for vg0900715492:

Variant ID: vg0900715492 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 715492
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAAGGGGGTTCCCAACCGGGAGTAAAAAGGGTTTCTCTACCAGTGAGTAACACAACACATGCATGGTAACAGCCATGAGTCTGAAACACGCGCTGCTAC[G/A]
AGAAAGTTTTTTCGTACGGTCAAATCCGATTTTTACATCTTACGGTAAAATCCGATTTTTACATCTTGGTGGACGGTCCGCACGCACCCAGGAGTCTGCA

Reverse complement sequence

TGCAGACTCCTGGGTGCGTGCGGACCGTCCACCAAGATGTAAAAATCGGATTTTACCGTAAGATGTAAAAATCGGATTTGACCGTACGAAAAAACTTTCT[C/T]
GTAGCAGCGCGTGTTTCAGACTCATGGCTGTTACCATGCATGTGTTGTGTTACTCACTGGTAGAGAAACCCTTTTTACTCCCGGTTGGGAACCCCCTTTA

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 97.40% 2.60% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 92.60% 7.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 92.50% 7.50% 0.00% 0.00% NA
Japonica Intermediate  241 75.10% 24.90% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0900715492 G -> A LOC_Os09g02020.1 upstream_gene_variant ; 4548.0bp to feature; MODIFIER silent_mutation Average:56.722; most accessible tissue: Minghui63 flag leaf, score: 70.17 N N N N
vg0900715492 G -> A LOC_Os09g02020-LOC_Os09g02030 intergenic_region ; MODIFIER silent_mutation Average:56.722; most accessible tissue: Minghui63 flag leaf, score: 70.17 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0900715492 3.01E-06 3.01E-06 mr1065 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
vg0900715492 4.62E-06 4.62E-06 mr1068 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
vg0900715492 NA 7.44E-06 mr1096 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
vg0900715492 7.43E-06 1.78E-06 mr1211 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
vg0900715492 1.36E-06 1.36E-06 mr1526 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