Search for Variation information by Variation ID:

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

Detailed information for vg0334524883:

Variant ID: vg0334524883 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34524883
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


TTATTTTTATGTTTTGATTGCTAGGTCCTAACATAAATGTGAGCTCAGTAAATGAAATCAACTACAGTGATAATTTTGTGGTTAGTAAATTGCTTGTGCT[C/G]
TTCTTATCATCTGTCTATTTAATTTTCTGAAAGAGAAAGATGTCTATTTATTCAGTATTTGCTTGATTGCTTGCAAGATCTCTTCCAGCTTTTCTCTTTC

Reverse complement sequence

GAAAGAGAAAAGCTGGAAGAGATCTTGCAAGCAATCAAGCAAATACTGAATAAATAGACATCTTTCTCTTTCAGAAAATTAAATAGACAGATGATAAGAA[G/C]
AGCACAAGCAATTTACTAACCACAAAATTATCACTGTAGTTGATTTCATTTACTGAGCTCACATTTATGTTAGGACCTAGCAATCAAAACATAAAAATAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.10% 1.20% 0.70% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.10% 3.80% 2.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 90.70% 5.50% 3.78% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 5.40% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0334524883 C -> G LOC_Os03g60730.2 3_prime_UTR_variant ; 440.0bp to feature; MODIFIER silent_mutation Average:37.951; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N
vg0334524883 C -> G LOC_Os03g60750.2 upstream_gene_variant ; 4300.0bp to feature; MODIFIER silent_mutation Average:37.951; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N
vg0334524883 C -> G LOC_Os03g60750.3 upstream_gene_variant ; 4293.0bp to feature; MODIFIER silent_mutation Average:37.951; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N
vg0334524883 C -> G LOC_Os03g60750.1 upstream_gene_variant ; 4299.0bp to feature; MODIFIER silent_mutation Average:37.951; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N
vg0334524883 C -> G LOC_Os03g60740.1 downstream_gene_variant ; 1598.0bp to feature; MODIFIER silent_mutation Average:37.951; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N
vg0334524883 C -> G LOC_Os03g60730.1 intron_variant ; MODIFIER silent_mutation Average:37.951; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334524883 2.21E-09 1.24E-12 Awn_length 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
vg0334524883 NA 9.72E-06 mr1757_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