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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1207302951:

Variant ID: vg1207302951 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7302951
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACCACCAAATCATTTTTTTTGTTCCTGTAGAGTGGGTGTGCTACCTAGTTTGTTACCTGAAGTTGGCATGGAATTCAATACTGTTGATGAGGCTTGGAT[G/A]
TTTTGGGTTAGCTATGGTGGTCAAAAAGGTTTCGAGGTTAGAAAAAGGTACTCAAACAAAAGGAAATCAGATGGAAAGGTTAGGTCATGCAGATATGTTT

Reverse complement sequence

AAACATATCTGCATGACCTAACCTTTCCATCTGATTTCCTTTTGTTTGAGTACCTTTTTCTAACCTCGAAACCTTTTTGACCACCATAGCTAACCCAAAA[C/T]
ATCCAAGCCTCATCAACAGTATTGAATTCCATGCCAACTTCAGGTAACAAACTAGGTAGCACACCCACTCTACAGGAACAAAAAAAATGATTTGGTGGTC

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 93.90% 5.70% 0.32% 0.00% NA
All Indica  2759 90.10% 9.40% 0.47% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.13% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 91.30% 8.60% 0.17% 0.00% NA
Indica II  465 87.70% 12.00% 0.22% 0.00% NA
Indica III  913 87.20% 12.30% 0.55% 0.00% NA
Indica Intermediate  786 94.10% 5.10% 0.76% 0.00% NA
Temperate Japonica  767 99.70% 0.00% 0.26% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 98.90% 1.10% 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
vg1207302951 G -> A LOC_Os12g13130.1 upstream_gene_variant ; 3702.0bp to feature; MODIFIER silent_mutation Average:16.998; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg1207302951 G -> A LOC_Os12g13130.4 upstream_gene_variant ; 3679.0bp to feature; MODIFIER silent_mutation Average:16.998; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg1207302951 G -> A LOC_Os12g13130.2 upstream_gene_variant ; 3679.0bp to feature; MODIFIER silent_mutation Average:16.998; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg1207302951 G -> A LOC_Os12g13130.3 upstream_gene_variant ; 3679.0bp to feature; MODIFIER silent_mutation Average:16.998; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg1207302951 G -> A LOC_Os12g13120.1 downstream_gene_variant ; 4629.0bp to feature; MODIFIER silent_mutation Average:16.998; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg1207302951 G -> A LOC_Os12g13120.2 downstream_gene_variant ; 1801.0bp to feature; MODIFIER silent_mutation Average:16.998; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N
vg1207302951 G -> A LOC_Os12g13120-LOC_Os12g13130 intergenic_region ; MODIFIER silent_mutation Average:16.998; most accessible tissue: Zhenshan97 flower, score: 31.8 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207302951 2.69E-06 NA mr1817 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
vg1207302951 1.65E-06 3.93E-06 mr1817 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
vg1207302951 NA 1.95E-07 mr1925 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
vg1207302951 NA 7.77E-06 mr1925 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