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Detailed information for vg1105648980:

Variant ID: vg1105648980 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5648980
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGGATTGAGATCCTCTGCAGTCAAATGTACGGTGTCTTTATCACTGACATGTGGGCTTCGACTGTAGAGTATTTTGATCCCTTGTGTTGTGGGGAGTC[G/A]
CCTATGATCGCAGCGCTCAGCACGACACTGATGCATGTAATCTTGTAGCTGGTATAATCTAATTTCCATTTTTCATAAAAAAATAAGGCTTGACTTGTGT

Reverse complement sequence

ACACAAGTCAAGCCTTATTTTTTTATGAAAAATGGAAATTAGATTATACCAGCTACAAGATTACATGCATCAGTGTCGTGCTGAGCGCTGCGATCATAGG[C/T]
GACTCCCCACAACACAAGGGATCAAAATACTCTACAGTCGAAGCCCACATGTCAGTGATAAAGACACCGTACATTTGACTGCAGAGGATCTCAATCCCAA

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 95.70% 4.30% 0.00% 0.00% NA
All Indica  2759 96.20% 3.80% 0.00% 0.00% NA
All Japonica  1512 94.00% 6.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.40% 11.60% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 91.40% 8.60% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1105648980 G -> A LOC_Os11g10400.1 upstream_gene_variant ; 564.0bp to feature; MODIFIER silent_mutation Average:77.321; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1105648980 G -> A LOC_Os11g10410.1 upstream_gene_variant ; 754.0bp to feature; MODIFIER silent_mutation Average:77.321; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1105648980 G -> A LOC_Os11g10400.2 upstream_gene_variant ; 564.0bp to feature; MODIFIER silent_mutation Average:77.321; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1105648980 G -> A LOC_Os11g10420.1 downstream_gene_variant ; 4223.0bp to feature; MODIFIER silent_mutation Average:77.321; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1105648980 G -> A LOC_Os11g10420.2 downstream_gene_variant ; 4223.0bp to feature; MODIFIER silent_mutation Average:77.321; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg1105648980 G -> A LOC_Os11g10400-LOC_Os11g10410 intergenic_region ; MODIFIER silent_mutation Average:77.321; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105648980 2.56E-06 NA mr1037_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