Search for Variation information by Variation ID:

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

Detailed information for vg0710495043:

Variant ID: vg0710495043 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10495043
Reference Allele: GAlternative Allele: C,A
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCGTTTCGGCGAGGGGAGGCAGCAACCGAGGGGCGGACGGTCTTCACCTCGCTCCTGCGATCCCGAGGGTAGCGACGGCGAGCGAAGGCGGCGATGGAC[G/C,A]
GCGACGAGCGGCACGGCTGAAAACGAGTCGACGGAAGATTGCCTCGGGTTGACAGCGACGACGAAGCTCCGATGGTTTGCAGCGGTGGCGAAGGGGTGGA

Reverse complement sequence

TCCACCCCTTCGCCACCGCTGCAAACCATCGGAGCTTCGTCGTCGCTGTCAACCCGAGGCAATCTTCCGTCGACTCGTTTTCAGCCGTGCCGCTCGTCGC[C/G,T]
GTCCATCGCCGCCTTCGCTCGCCGTCGCTACCCTCGGGATCGCAGGAGCGAGGTGAAGACCGTCCGCCCCTCGGTTGCTGCCTCCCCTCGCCGAAACGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.50% 3.60% 0.97% 3.62% A: 0.32%
All Indica  2759 99.90% 0.00% 0.07% 0.00% A: 0.04%
All Japonica  1512 79.70% 11.20% 1.12% 7.87% A: 0.13%
Aus  269 82.90% 0.00% 1.12% 15.61% A: 0.37%
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 99.90% 0.00% 0.00% 0.00% A: 0.11%
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 74.10% 17.60% 1.83% 6.52% NA
Tropical Japonica  504 85.50% 0.20% 0.20% 13.69% A: 0.40%
Japonica Intermediate  241 85.50% 13.70% 0.83% 0.00% NA
VI/Aromatic  96 59.40% 1.00% 20.83% 9.38% A: 9.38%
Intermediate  90 92.20% 0.00% 4.44% 1.11% A: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0710495043 G -> DEL N N silent_mutation Average:51.663; most accessible tissue: Callus, score: 93.013 N N N N
vg0710495043 G -> A LOC_Os07g17760.1 upstream_gene_variant ; 2499.0bp to feature; MODIFIER silent_mutation Average:51.663; most accessible tissue: Callus, score: 93.013 N N N N
vg0710495043 G -> A LOC_Os07g17770.1 upstream_gene_variant ; 4722.0bp to feature; MODIFIER silent_mutation Average:51.663; most accessible tissue: Callus, score: 93.013 N N N N
vg0710495043 G -> A LOC_Os07g17760-LOC_Os07g17770 intergenic_region ; MODIFIER silent_mutation Average:51.663; most accessible tissue: Callus, score: 93.013 N N N N
vg0710495043 G -> C LOC_Os07g17760.1 upstream_gene_variant ; 2499.0bp to feature; MODIFIER silent_mutation Average:51.663; most accessible tissue: Callus, score: 93.013 N N N N
vg0710495043 G -> C LOC_Os07g17770.1 upstream_gene_variant ; 4722.0bp to feature; MODIFIER silent_mutation Average:51.663; most accessible tissue: Callus, score: 93.013 N N N N
vg0710495043 G -> C LOC_Os07g17760-LOC_Os07g17770 intergenic_region ; MODIFIER silent_mutation Average:51.663; most accessible tissue: Callus, score: 93.013 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710495043 NA 4.08E-09 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
vg0710495043 NA 3.11E-09 mr1549 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
vg0710495043 NA 1.06E-09 mr1624 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
vg0710495043 NA 9.77E-06 mr1677 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
vg0710495043 NA 8.95E-06 mr1057_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