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Detailed information for vg0920611854:

Variant ID: vg0920611854 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20611854
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAGTGTACTCACAATATTTCACTATGTATAGATCTAATGATGTAGTGAACTGAAATATTCCATTGCAACAAAAAAACGCACATATTTTGGAAACCCCCT[G/A]
TTAAGGGAATTCGTTTCATTTTTTGTTCCAAAAAAAATATTTCACCTAGTGTACTTATAATGTTTCACTATGAATGGATCAAATGTTGCAGTGAACTGAA

Reverse complement sequence

TTCAGTTCACTGCAACATTTGATCCATTCATAGTGAAACATTATAAGTACACTAGGTGAAATATTTTTTTTGGAACAAAAAATGAAACGAATTCCCTTAA[C/T]
AGGGGGTTTCCAAAATATGTGCGTTTTTTTGTTGCAATGGAATATTTCAGTTCACTACATCATTAGATCTATACATAGTGAAATATTGTGAGTACACTAG

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 94.60% 5.40% 0.00% 0.00% NA
All Indica  2759 92.10% 7.90% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 90.00% 10.00% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 91.40% 8.60% 0.00% 0.00% NA
Indica III  913 90.80% 9.20% 0.00% 0.00% NA
Indica Intermediate  786 88.70% 11.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0920611854 G -> A LOC_Os09g35810.1 upstream_gene_variant ; 2484.0bp to feature; MODIFIER silent_mutation Average:34.555; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0920611854 G -> A LOC_Os09g35830.3 upstream_gene_variant ; 1534.0bp to feature; MODIFIER silent_mutation Average:34.555; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0920611854 G -> A LOC_Os09g35810.2 upstream_gene_variant ; 2484.0bp to feature; MODIFIER silent_mutation Average:34.555; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0920611854 G -> A LOC_Os09g35830.1 upstream_gene_variant ; 1534.0bp to feature; MODIFIER silent_mutation Average:34.555; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0920611854 G -> A LOC_Os09g35830.2 upstream_gene_variant ; 1534.0bp to feature; MODIFIER silent_mutation Average:34.555; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0920611854 G -> A LOC_Os09g35830.4 upstream_gene_variant ; 1534.0bp to feature; MODIFIER silent_mutation Average:34.555; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0920611854 G -> A LOC_Os09g35820.1 downstream_gene_variant ; 1248.0bp to feature; MODIFIER silent_mutation Average:34.555; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0920611854 G -> A LOC_Os09g35820-LOC_Os09g35830 intergenic_region ; MODIFIER silent_mutation Average:34.555; 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
vg0920611854 2.71E-06 2.71E-06 mr1313_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
vg0920611854 6.29E-06 6.29E-06 mr1473_2 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
vg0920611854 NA 4.97E-06 mr1849_2 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