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Detailed information for vg0726031887:

Variant ID: vg0726031887 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26031887
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


AGGGTTTAGGGTTAGAGTTGAGGGGAGGGGGTGGAGATCGCTAAGCTTACATGCATGGCCGTAGGAGGCAGCGGTGAACGCAAATGACGAGTATGGCACT[A/G]
GAGTTGCAAGGATGGAGGAGGATGATGGGCCGGAGTTGGTTAGGGTTGGGGGGAGGGGGTGGAGATCGCTAAGCTTACATGCATGACCGTGGGAGGCAGC

Reverse complement sequence

GCTGCCTCCCACGGTCATGCATGTAAGCTTAGCGATCTCCACCCCCTCCCCCCAACCCTAACCAACTCCGGCCCATCATCCTCCTCCATCCTTGCAACTC[T/C]
AGTGCCATACTCGTCATTTGCGTTCACCGCTGCCTCCTACGGCCATGCATGTAAGCTTAGCGATCTCCACCCCCTCCCCTCAACTCTAACCCTAAACCCT

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 62.00% 1.00% 3.87% 33.11% NA
All Indica  2759 43.90% 1.70% 6.42% 47.99% NA
All Japonica  1512 97.00% 0.00% 0.00% 2.98% NA
Aus  269 31.20% 0.40% 2.23% 66.17% NA
Indica I  595 71.40% 0.50% 6.05% 22.02% NA
Indica II  465 29.70% 1.10% 2.80% 66.45% NA
Indica III  913 28.40% 3.40% 6.90% 61.34% NA
Indica Intermediate  786 49.60% 0.90% 8.27% 41.22% NA
Temperate Japonica  767 97.40% 0.00% 0.00% 2.61% NA
Tropical Japonica  504 96.80% 0.00% 0.00% 3.17% NA
Japonica Intermediate  241 96.30% 0.00% 0.00% 3.73% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 82.20% 0.00% 0.00% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0726031887 A -> DEL N N silent_mutation Average:58.367; most accessible tissue: Zhenshan97 root, score: 81.351 N N N N
vg0726031887 A -> G LOC_Os07g43480.1 upstream_gene_variant ; 3627.0bp to feature; MODIFIER silent_mutation Average:58.367; most accessible tissue: Zhenshan97 root, score: 81.351 N N N N
vg0726031887 A -> G LOC_Os07g43490.1 upstream_gene_variant ; 586.0bp to feature; MODIFIER silent_mutation Average:58.367; most accessible tissue: Zhenshan97 root, score: 81.351 N N N N
vg0726031887 A -> G LOC_Os07g43500.1 downstream_gene_variant ; 1298.0bp to feature; MODIFIER silent_mutation Average:58.367; most accessible tissue: Zhenshan97 root, score: 81.351 N N N N
vg0726031887 A -> G LOC_Os07g43510.1 downstream_gene_variant ; 4201.0bp to feature; MODIFIER silent_mutation Average:58.367; most accessible tissue: Zhenshan97 root, score: 81.351 N N N N
vg0726031887 A -> G LOC_Os07g43490-LOC_Os07g43500 intergenic_region ; MODIFIER silent_mutation Average:58.367; most accessible tissue: Zhenshan97 root, score: 81.351 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726031887 1.09E-06 7.28E-13 mr1004_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
vg0726031887 4.17E-06 3.12E-08 mr1004_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