Search for Variation information by Variation ID:

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

Detailed information for vg0713017347:

Variant ID: vg0713017347 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 13017347
Reference Allele: AAlternative Allele: G,T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACAAGAACTCCCCCAAGATAAAGATGAAGCCGAGCGGATTTCCAGGCGCAGCAAACTCTATGTTATTCATGAGACCGAGTTGTACAAGAAAAGTCCATC[A/G,T]
GGAATCCTGCAACGCTGTGTGTCTTTGGAGGAGGGAAGGCAATTGCTAAAAGATATACATTCAGGCATCTGTGGTAATCACGCTGCTGCACGAACCATCG

Reverse complement sequence

CGATGGTTCGTGCAGCAGCGTGATTACCACAGATGCCTGAATGTATATCTTTTAGCAATTGCCTTCCCTCCTCCAAAGACACACAGCGTTGCAGGATTCC[T/C,A]
GATGGACTTTTCTTGTACAACTCGGTCTCATGAATAACATAGAGTTTGCTGCGCCTGGAAATCCGCTCGGCTTCATCTTTATCTTGGGGGAGTTCTTGTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.80% 0.10% 11.79% 38.17% G: 0.06%
All Indica  2759 28.90% 0.20% 15.98% 54.87% G: 0.07%
All Japonica  1512 84.90% 0.10% 6.28% 8.66% G: 0.07%
Aus  269 56.50% 0.00% 2.97% 40.52% NA
Indica I  595 50.30% 0.00% 4.37% 45.21% G: 0.17%
Indica II  465 20.60% 0.00% 21.08% 58.06% G: 0.22%
Indica III  913 15.20% 0.00% 19.61% 65.17% NA
Indica Intermediate  786 33.50% 0.60% 17.56% 48.35% NA
Temperate Japonica  767 83.20% 0.10% 7.04% 9.52% G: 0.13%
Tropical Japonica  504 87.30% 0.00% 4.17% 8.53% NA
Japonica Intermediate  241 85.50% 0.00% 8.30% 6.22% NA
VI/Aromatic  96 72.90% 1.00% 6.25% 19.79% NA
Intermediate  90 57.80% 0.00% 7.78% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0713017347 A -> DEL N N silent_mutation Average:9.138; most accessible tissue: Callus, score: 17.081 N N N N
vg0713017347 A -> G LOC_Os07g23090.1 upstream_gene_variant ; 3266.0bp to feature; MODIFIER silent_mutation Average:9.138; most accessible tissue: Callus, score: 17.081 N N N N
vg0713017347 A -> G LOC_Os07g23080.1 downstream_gene_variant ; 1634.0bp to feature; MODIFIER silent_mutation Average:9.138; most accessible tissue: Callus, score: 17.081 N N N N
vg0713017347 A -> G LOC_Os07g23070.1 intron_variant ; MODIFIER silent_mutation Average:9.138; most accessible tissue: Callus, score: 17.081 N N N N
vg0713017347 A -> T LOC_Os07g23090.1 upstream_gene_variant ; 3266.0bp to feature; MODIFIER silent_mutation Average:9.138; most accessible tissue: Callus, score: 17.081 N N N N
vg0713017347 A -> T LOC_Os07g23080.1 downstream_gene_variant ; 1634.0bp to feature; MODIFIER silent_mutation Average:9.138; most accessible tissue: Callus, score: 17.081 N N N N
vg0713017347 A -> T LOC_Os07g23070.1 intron_variant ; MODIFIER silent_mutation Average:9.138; most accessible tissue: Callus, score: 17.081 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0713017347 NA 9.28E-11 Awn_length Jap_All Not 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
vg0713017347 NA 5.12E-10 mr1549 Jap_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
vg0713017347 NA 2.46E-09 mr1624 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