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Detailed information for vg0507616861:

Variant ID: vg0507616861 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7616861
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


TCATAATTTTCAAATGTTATGAATGGTTGGAAATATTTCAACTCACACATTTCAAAATTGCTCCAAAAATCAAATTTTTGTTGAATTTTATTGTGTGGGG[A/G]
TAGCCGAACTGTGTAAGAGCTGTGCACAGGCGGCTGGGGGCCAGGCGGTCTGACCGGCCTCATATAGCCGGTCTGACCGGCCGGGGATGGTGGGCCCAGG

Reverse complement sequence

CCTGGGCCCACCATCCCCGGCCGGTCAGACCGGCTATATGAGGCCGGTCAGACCGCCTGGCCCCCAGCCGCCTGTGCACAGCTCTTACACAGTTCGGCTA[T/C]
CCCCACACAATAAAATTCAACAAAAATTTGATTTTTGGAGCAATTTTGAAATGTGTGAGTTGAAATATTTCCAACCATTCATAACATTTGAAAATTATGA

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 60.70% 20.90% 18.41% 0.00% NA
All Indica  2759 35.40% 35.00% 29.58% 0.00% NA
All Japonica  1512 98.90% 0.30% 0.79% 0.00% NA
Aus  269 87.40% 4.10% 8.55% 0.00% NA
Indica I  595 24.40% 41.70% 33.95% 0.00% NA
Indica II  465 40.40% 20.90% 38.71% 0.00% NA
Indica III  913 35.90% 41.20% 22.89% 0.00% NA
Indica Intermediate  786 40.10% 31.30% 28.63% 0.00% NA
Temperate Japonica  767 98.30% 0.70% 1.04% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.60% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 4.40% 21.11% 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
vg0507616861 A -> G LOC_Os05g13740.1 downstream_gene_variant ; 700.0bp to feature; MODIFIER silent_mutation Average:67.867; most accessible tissue: Minghui63 flag leaf, score: 81.566 N N N N
vg0507616861 A -> G LOC_Os05g13750.1 downstream_gene_variant ; 3159.0bp to feature; MODIFIER silent_mutation Average:67.867; most accessible tissue: Minghui63 flag leaf, score: 81.566 N N N N
vg0507616861 A -> G LOC_Os05g13740-LOC_Os05g13750 intergenic_region ; MODIFIER silent_mutation Average:67.867; most accessible tissue: Minghui63 flag leaf, score: 81.566 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507616861 NA 1.35E-06 mr1321 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
vg0507616861 NA 1.02E-08 mr1465 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
vg0507616861 7.09E-07 7.09E-07 mr1894 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
vg0507616861 NA 5.45E-13 mr1514_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