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Detailed information for vg0516784260:

Variant ID: vg0516784260 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 16784260
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGTATAGATTATAGAATATGGATTTGGTTGGATGTTTTTCTTAGACCAATACTTAGGGCTCATTTTGATCAAGAGAGATTAGGCCCAAAAAATTGAATC[A/G]
AAATCCCTGCTCATCCCATGGAATTTGGTTTAGCCTTTTCCTATCCAACCAAGAACAGTTCAACATTCATACACTTGAGTTTCCTAACCAGAAAATACTA

Reverse complement sequence

TAGTATTTTCTGGTTAGGAAACTCAAGTGTATGAATGTTGAACTGTTCTTGGTTGGATAGGAAAAGGCTAAACCAAATTCCATGGGATGAGCAGGGATTT[T/C]
GATTCAATTTTTTGGGCCTAATCTCTCTTGATCAAAATGAGCCCTAAGTATTGGTCTAAGAAAAACATCCAACCAAATCCATATTCTATAATCTATACTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.00% 4.00% 1.97% 0.00% NA
All Indica  2759 90.50% 6.20% 3.23% 0.00% NA
All Japonica  1512 98.90% 0.80% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 75.10% 14.30% 10.59% 0.00% NA
Indica II  465 87.10% 11.80% 1.08% 0.00% NA
Indica III  913 99.70% 0.00% 0.33% 0.00% NA
Indica Intermediate  786 93.60% 4.10% 2.29% 0.00% NA
Temperate Japonica  767 98.20% 1.40% 0.39% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0516784260 A -> G LOC_Os05g28630.1 intron_variant ; MODIFIER silent_mutation Average:58.765; most accessible tissue: Callus, score: 73.567 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0516784260 2.88E-06 2.88E-06 mr1171_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
vg0516784260 3.10E-06 9.06E-09 mr1645_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
vg0516784260 NA 2.65E-07 mr1645_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
vg0516784260 1.36E-06 1.73E-07 mr1647_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
vg0516784260 5.10E-06 1.29E-06 mr1647_2 Ind_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
vg0516784260 NA 6.17E-06 mr1655_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