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Detailed information for vg0407736903:

Variant ID: vg0407736903 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7736903
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACAGATGTTTAACAGAGAAAAAGGAAAGAATGTCAGCGGGTATGCCTCCAGTAACTCAAGTTTTCAACTCAATCCACCATTGGCCTCAAGAGAGTTAAC[A/C]
AGGGCACACCCTTGGTCCATTCCAAGCATGCTGCTTAGTTCACAGCTACCATTGGTTGGAAGTCAAGACCAAAATCAGTATGTGTTTGATCGAGCATTTG

Reverse complement sequence

CAAATGCTCGATCAAACACATACTGATTTTGGTCTTGACTTCCAACCAATGGTAGCTGTGAACTAAGCAGCATGCTTGGAATGGACCAAGGGTGTGCCCT[T/G]
GTTAACTCTCTTGAGGCCAATGGTGGATTGAGTTGAAAACTTGAGTTACTGGAGGCATACCCGCTGACATTCTTTCCTTTTTCTCTGTTAAACATCTGTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.50% 0.30% 0.19% 0.00% NA
All Indica  2759 99.20% 0.50% 0.33% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.10% 1.50% 0.43% 0.00% NA
Indica III  913 98.70% 0.50% 0.77% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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
vg0407736903 A -> C LOC_Os04g13870.1 synonymous_variant ; p.Thr95Thr; LOW N Average:11.785; most accessible tissue: Zhenshan97 flag leaf, score: 16.47 N N N N
vg0407736903 A -> C LOC_Os04g13874.1 downstream_gene_variant ; 3754.0bp to feature; MODIFIER N Average:11.785; most accessible tissue: Zhenshan97 flag leaf, score: 16.47 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407736903 5.18E-07 NA mr1754_2 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
vg0407736903 3.75E-06 4.60E-06 mr1754_2 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