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Detailed information for vg1117878765:

Variant ID: vg1117878765 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17878765
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCCGTCACTATATATATATATATATATATATCGCCTCCTGTAACTCCCTCAATTGAGGGTTTAGCCTGACGTGGTATGTAAAGAAGCAAGGGCGGAACT[G/A]
TGCCTAGAGCAGCTTGGACCCGAGCTCTACTCATGAGAATTTTTAGTGAACTGGTACCTATATTTTTTTTCAGATTTTCCTAACCACTCATGTTGCCCAG

Reverse complement sequence

CTGGGCAACATGAGTGGTTAGGAAAATCTGAAAAAAAATATAGGTACCAGTTCACTAAAAATTCTCATGAGTAGAGCTCGGGTCCAAGCTGCTCTAGGCA[C/T]
AGTTCCGCCCTTGCTTCTTTACATACCACGTCAGGCTAAACCCTCAATTGAGGGAGTTACAGGAGGCGATATATATATATATATATATATAGTGACGGAC

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 97.80% 1.70% 0.51% 0.00% NA
All Indica  2759 96.60% 2.90% 0.58% 0.00% NA
All Japonica  1512 99.50% 0.10% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 87.70% 10.10% 2.18% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 2.20% 0.38% 0.00% NA
Temperate Japonica  767 99.00% 0.30% 0.78% 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 97.80% 0.00% 2.22% 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
vg1117878765 G -> A LOC_Os11g30690.1 upstream_gene_variant ; 4027.0bp to feature; MODIFIER silent_mutation Average:68.432; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N
vg1117878765 G -> A LOC_Os11g30700.1 downstream_gene_variant ; 658.0bp to feature; MODIFIER silent_mutation Average:68.432; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N
vg1117878765 G -> A LOC_Os11g30690-LOC_Os11g30700 intergenic_region ; MODIFIER silent_mutation Average:68.432; most accessible tissue: Zhenshan97 young leaf, score: 84.814 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117878765 NA 8.10E-08 mr1002_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
vg1117878765 5.95E-07 5.95E-07 mr1335_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
vg1117878765 NA 2.92E-07 mr1864_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