Search for Variation information by Variation ID:

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

Detailed information for vg1126395505:

Variant ID: vg1126395505 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26395505
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.52, G: 0.48, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GTCATCGTTGCGGTGAGCGTCGTTATCCTGTTCCACCCACCTGGCGGAGTTTGGAGTGGCTCTCCTCAGCCCCCGTCACCGCACTGACCCGAGGGTCCCG[A/G]
TGGTCCATAGCCTCCGTGTCATCGTCGTTGCGGGCACTGTCATCGCGAGCGGTCGTCATCATCGCGTAACACCCGCCGGGCGAAGCTCGGAGTGGCTCTC

Reverse complement sequence

GAGAGCCACTCCGAGCTTCGCCCGGCGGGTGTTACGCGATGATGACGACCGCTCGCGATGACAGTGCCCGCAACGACGATGACACGGAGGCTATGGACCA[T/C]
CGGGACCCTCGGGTCAGTGCGGTGACGGGGGCTGAGGAGAGCCACTCCAAACTCCGCCAGGTGGGTGGAACAGGATAACGACGCTCACCGCAACGATGAC

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 56.70% 43.00% 0.21% 0.00% NA
All Indica  2759 38.60% 61.10% 0.33% 0.00% NA
All Japonica  1512 86.30% 13.60% 0.07% 0.00% NA
Aus  269 57.20% 42.80% 0.00% 0.00% NA
Indica I  595 49.40% 50.60% 0.00% 0.00% NA
Indica II  465 50.50% 48.60% 0.86% 0.00% NA
Indica III  913 19.90% 80.10% 0.00% 0.00% NA
Indica Intermediate  786 45.00% 54.30% 0.64% 0.00% NA
Temperate Japonica  767 92.30% 7.60% 0.13% 0.00% NA
Tropical Japonica  504 81.00% 19.00% 0.00% 0.00% NA
Japonica Intermediate  241 78.40% 21.60% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg1126395505 A -> G LOC_Os11g43710.1 synonymous_variant ; p.His20His; LOW synonymous_codon Average:68.697; most accessible tissue: Zhenshan97 young leaf, score: 88.878 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126395505 NA 1.38E-06 mr1121 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
vg1126395505 NA 6.15E-08 mr1191_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
vg1126395505 NA 1.53E-06 mr1662_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