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Detailed information for vg1002061060:

Variant ID: vg1002061060 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2061060
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGACTTTGAGATTAGTGCTATTAAGTAAGACGAAAATAAAAGGGTGAATAGTCAGTTAACTCCTTTAACTTTTGCTCAGAGGTCGAATTAGTCCTGGAT[A/G]
CTTTATAATATCCAAACAAGACCCTACAAATATCATGCGGCTTAATATAGTCCTTAAACTCACTTAAAACGCCATATGGACATGCCACATCATTTGTGCT

Reverse complement sequence

AGCACAAATGATGTGGCATGTCCATATGGCGTTTTAAGTGAGTTTAAGGACTATATTAAGCCGCATGATATTTGTAGGGTCTTGTTTGGATATTATAAAG[T/C]
ATCCAGGACTAATTCGACCTCTGAGCAAAAGTTAAAGGAGTTAACTGACTATTCACCCTTTTATTTTCGTCTTACTTAATAGCACTAATCTCAAAGTCAA

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 91.00% 7.90% 1.14% 0.00% NA
All Indica  2759 99.30% 0.50% 0.22% 0.00% NA
All Japonica  1512 74.20% 22.70% 3.11% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.20% 0.67% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 99.60% 0.30% 0.11% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 66.00% 29.10% 4.95% 0.00% NA
Tropical Japonica  504 94.80% 5.20% 0.00% 0.00% NA
Japonica Intermediate  241 57.30% 39.00% 3.73% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 86.70% 12.20% 1.11% 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
vg1002061060 A -> G LOC_Os10g04370.1 upstream_gene_variant ; 243.0bp to feature; MODIFIER silent_mutation Average:46.393; most accessible tissue: Callus, score: 85.002 N N N N
vg1002061060 A -> G LOC_Os10g04370.2 upstream_gene_variant ; 243.0bp to feature; MODIFIER silent_mutation Average:46.393; most accessible tissue: Callus, score: 85.002 N N N N
vg1002061060 A -> G LOC_Os10g04342.1 downstream_gene_variant ; 3501.0bp to feature; MODIFIER silent_mutation Average:46.393; most accessible tissue: Callus, score: 85.002 N N N N
vg1002061060 A -> G LOC_Os10g04380.1 downstream_gene_variant ; 1433.0bp to feature; MODIFIER silent_mutation Average:46.393; most accessible tissue: Callus, score: 85.002 N N N N
vg1002061060 A -> G LOC_Os10g04370-LOC_Os10g04380 intergenic_region ; MODIFIER silent_mutation Average:46.393; most accessible tissue: Callus, score: 85.002 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002061060 8.74E-07 NA mr1926 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
vg1002061060 2.60E-06 3.87E-10 mr1959 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
vg1002061060 3.26E-07 NA mr1310_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
vg1002061060 3.94E-07 NA mr1959_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