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Detailed information for vg0707853841:

Variant ID: vg0707853841 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 7853841
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTGATGCTGACAAGATTGTGCGGACATGCGAAGGTTGTCAATTTTTTGCCAGACAAATTCATCTGCCAGCCCAAGAGTTGCAAACCATCCCGTTGTCCT[A/G]
GCCGTTTGCGTTCTGGGGGCTTGACATGGTCGGCCCGTTTAAAAGGGCAGTCGGCGGTTACACGCATCTCTTTGTGGCTATCGACAAATTCTCCAAGTGG

Reverse complement sequence

CCACTTGGAGAATTTGTCGATAGCCACAAAGAGATGCGTGTAACCGCCGACTGCCCTTTTAAACGGGCCGACCATGTCAAGCCCCCAGAACGCAAACGGC[T/C]
AGGACAACGGGATGGTTTGCAACTCTTGGGCTGGCAGATGAATTTGTCTGGCAAAAAATTGACAACCTTCGCATGTCCGCACAATCTTGTCAGCATCAGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.20% 0.06% 0.00% NA
All Indica  2759 99.70% 0.20% 0.11% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0707853841 A -> G LOC_Os07g13680.1 downstream_gene_variant ; 374.0bp to feature; MODIFIER N Average:14.269; most accessible tissue: Zhenshan97 flower, score: 19.853 N N N N
vg0707853841 A -> G LOC_Os07g13690.1 downstream_gene_variant ; 1190.0bp to feature; MODIFIER N Average:14.269; most accessible tissue: Zhenshan97 flower, score: 19.853 N N N N
vg0707853841 A -> G LOC_Os07g13680-LOC_Os07g13690 intergenic_region ; MODIFIER N Average:14.269; most accessible tissue: Zhenshan97 flower, score: 19.853 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0707853841 1.31E-06 1.73E-06 mr1066 Ind_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
vg0707853841 1.23E-06 1.23E-06 mr1105 Ind_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
vg0707853841 NA 6.49E-06 mr1232 Ind_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
vg0707853841 5.19E-07 9.68E-07 mr1606 Ind_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