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Detailed information for vg1010726638:

Variant ID: vg1010726638 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10726638
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTACATGCAAGTTGCATATAAGTTATAAAATTTAGTTTAAAATATAATTACACTATATTTGCACTATAACGTTATATTTAATATATTTCCACCCAAAAA[G/A]
TTATCGCAGCACTTTTAGAGTGGTCTTTACTATAAGTCATCGGGATCGAGTGACACCAATGTTAATTGTTAATTGTTAGCCTGTCAATATAGATCCACCC

Reverse complement sequence

GGGTGGATCTATATTGACAGGCTAACAATTAACAATTAACATTGGTGTCACTCGATCCCGATGACTTATAGTAAAGACCACTCTAAAAGTGCTGCGATAA[C/T]
TTTTTGGGTGGAAATATATTAAATATAACGTTATAGTGCAAATATAGTGTAATTATATTTTAAACTAAATTTTATAACTTATATGCAACTTGCATGTAAT

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 92.70% 7.30% 0.00% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 78.90% 21.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 71.80% 28.20% 0.00% 0.00% NA
Tropical Japonica  504 82.10% 17.90% 0.00% 0.00% NA
Japonica Intermediate  241 94.60% 5.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1010726638 G -> A LOC_Os10g21110.1 upstream_gene_variant ; 679.0bp to feature; MODIFIER silent_mutation Average:37.548; most accessible tissue: Callus, score: 53.194 N N N N
vg1010726638 G -> A LOC_Os10g21100-LOC_Os10g21110 intergenic_region ; MODIFIER silent_mutation Average:37.548; most accessible tissue: Callus, score: 53.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010726638 4.17E-06 4.63E-09 mr1645_2 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
vg1010726638 1.40E-06 9.92E-08 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
vg1010726638 6.61E-06 6.61E-06 mr1647_2 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