Search for Variation information by Variation ID:

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

Detailed information for vg0726108448:

Variant ID: vg0726108448 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26108448
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCTAGTATGCTTTTTGATTGCCAAAAATCAGTCAAGGGTTTGATTGTCTAGATATTATGTTTCTTTTCATACTTAGTGCTGCATCAGTTAAGTTTGAT[C/A]
TACTAAATTCGTGTTTAGAACCATATTTCCTAGCCTGTTTTTTGATTGCCAATAAGGGTTTCATCGGGATTTCAGCCGATGAGTTGTCCCTAGCCTGGTT

Reverse complement sequence

AACCAGGCTAGGGACAACTCATCGGCTGAAATCCCGATGAAACCCTTATTGGCAATCAAAAAACAGGCTAGGAAATATGGTTCTAAACACGAATTTAGTA[G/T]
ATCAAACTTAACTGATGCAGCACTAAGTATGAAAAGAAACATAATATCTAGACAATCAAACCCTTGACTGATTTTTGGCAATCAAAAAGCATACTAGGAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.50% 14.50% 0.02% 0.00% NA
All Indica  2759 77.60% 22.40% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 77.70% 22.30% 0.00% 0.00% NA
Indica I  595 90.60% 9.40% 0.00% 0.00% NA
Indica II  465 91.00% 9.00% 0.00% 0.00% NA
Indica III  913 59.90% 40.10% 0.00% 0.00% NA
Indica Intermediate  786 80.50% 19.50% 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 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0726108448 C -> A LOC_Os07g43604.1 upstream_gene_variant ; 3757.0bp to feature; MODIFIER silent_mutation Average:27.049; most accessible tissue: Zhenshan97 young leaf, score: 39.169 N N N N
vg0726108448 C -> A LOC_Os07g43610.1 intron_variant ; MODIFIER silent_mutation Average:27.049; most accessible tissue: Zhenshan97 young leaf, score: 39.169 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726108448 NA 1.11E-09 mr1155_2 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
vg0726108448 NA 2.73E-06 mr1246_2 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
vg0726108448 3.87E-06 NA mr1521_2 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
vg0726108448 2.60E-06 NA mr1726_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
vg0726108448 4.44E-06 NA mr1934_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
vg0726108448 6.82E-06 NA mr1950_2 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