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Detailed information for vg0114706624:

Variant ID: vg0114706624 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14706624
Reference Allele: CAlternative Allele: T,A,G
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATCTAGATCAAAAATTTTTATTTTGGTCATTTGTTCATCCGACAAAGTAATTTTAGTATTGTTTACAAAATTTACATATCTCTTATATGGTTTTATAAA[C/T,A,G]
TATAAGAGAGATATGTAAATTTTGTGAACAATGTTACTATCACTTTGTCGGAAGAAGAAATGACCAAAATAAAAGTTATAGATATTGATGAGTTATATAA

Reverse complement sequence

TTATATAACTCATCAATATCTATAACTTTTATTTTGGTCATTTCTTCTTCCGACAAAGTGATAGTAACATTGTTCACAAAATTTACATATCTCTCTTATA[G/A,T,C]
TTTATAAAACCATATAAGAGATATGTAAATTTTGTAAACAATACTAAAATTACTTTGTCGGATGAACAAATGACCAAAATAAAAATTTTTGATCTAGATG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.30% 0.80% 1.44% 0.00% T: 0.51%
All Indica  2759 98.70% 1.30% 0.00% 0.00% NA
All Japonica  1512 94.30% 0.00% 4.17% 0.00% T: 1.52%
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 90.20% 0.00% 6.78% 0.00% T: 3.00%
Tropical Japonica  504 99.40% 0.00% 0.60% 0.00% NA
Japonica Intermediate  241 96.70% 0.00% 3.32% 0.00% NA
VI/Aromatic  96 96.90% 0.00% 3.12% 0.00% NA
Intermediate  90 96.70% 1.10% 1.11% 0.00% T: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0114706624 C -> G LOC_Os01g25920.1 upstream_gene_variant ; 1010.0bp to feature; MODIFIER N Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> G LOC_Os01g25930.1 upstream_gene_variant ; 1196.0bp to feature; MODIFIER N Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> G LOC_Os01g25920.2 upstream_gene_variant ; 626.0bp to feature; MODIFIER N Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> G LOC_Os01g25920.3 upstream_gene_variant ; 626.0bp to feature; MODIFIER N Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> G LOC_Os01g25910.1 downstream_gene_variant ; 4555.0bp to feature; MODIFIER N Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> G LOC_Os01g25920-LOC_Os01g25930 intergenic_region ; MODIFIER N Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> T LOC_Os01g25920.1 upstream_gene_variant ; 1010.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> T LOC_Os01g25930.1 upstream_gene_variant ; 1196.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> T LOC_Os01g25920.2 upstream_gene_variant ; 626.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> T LOC_Os01g25920.3 upstream_gene_variant ; 626.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> T LOC_Os01g25910.1 downstream_gene_variant ; 4555.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> T LOC_Os01g25920-LOC_Os01g25930 intergenic_region ; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> A LOC_Os01g25920.1 upstream_gene_variant ; 1010.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> A LOC_Os01g25930.1 upstream_gene_variant ; 1196.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> A LOC_Os01g25920.2 upstream_gene_variant ; 626.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> A LOC_Os01g25920.3 upstream_gene_variant ; 626.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> A LOC_Os01g25910.1 downstream_gene_variant ; 4555.0bp to feature; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0114706624 C -> A LOC_Os01g25920-LOC_Os01g25930 intergenic_region ; MODIFIER silent_mutation Average:21.773; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114706624 2.04E-07 NA Plant_height Jap_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0114706624 NA 1.79E-06 mr1164_2 Jap_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
vg0114706624 NA 2.98E-06 mr1221_2 Jap_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
vg0114706624 NA 4.32E-06 mr1913_2 Jap_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