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Detailed information for vg1017150631:

Variant ID: vg1017150631 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17150631
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 377. )

Flanking Sequence (100 bp) in Reference Genome:


ACATGAAAATACACAAGATAGTACAAGTGATCATACAATGGGAGACATGATAGCACAACTAGGCAAATAAGGAGATAAGCATCACAATCACAAAGATAAA[G/A]
AGAGTGAGAGGAGACAAACGATTTGTTTCCCGAAGTTCGGATTCTCCACCGAGAATCCTACGTCTCCGTTGAGGAGCTCCAAAGAGCCAGGTCTTGATTA

Reverse complement sequence

TAATCAAGACCTGGCTCTTTGGAGCTCCTCAACGGAGACGTAGGATTCTCGGTGGAGAATCCGAACTTCGGGAAACAAATCGTTTGTCTCCTCTCACTCT[C/T]
TTTATCTTTGTGATTGTGATGCTTATCTCCTTATTTGCCTAGTTGTGCTATCATGTCTCCCATTGTATGATCACTTGTACTATCTTGTGTATTTTCATGT

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 95.80% 4.20% 0.00% 0.00% NA
All Indica  2759 93.10% 6.90% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.40% 16.60% 0.00% 0.00% NA
Indica II  465 92.70% 7.30% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 93.30% 6.70% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1017150631 G -> A LOC_Os10g32740.1 upstream_gene_variant ; 4810.0bp to feature; MODIFIER silent_mutation Average:28.701; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg1017150631 G -> A LOC_Os10g32750.1 downstream_gene_variant ; 2314.0bp to feature; MODIFIER silent_mutation Average:28.701; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg1017150631 G -> A LOC_Os10g32760.1 downstream_gene_variant ; 4711.0bp to feature; MODIFIER silent_mutation Average:28.701; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg1017150631 G -> A LOC_Os10g32740-LOC_Os10g32750 intergenic_region ; MODIFIER silent_mutation Average:28.701; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017150631 3.55E-07 1.25E-07 mr1745 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
vg1017150631 NA 1.14E-06 mr1974 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