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Detailed information for vg1126391061:

Variant ID: vg1126391061 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26391061
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, C: 0.20, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


TTACGATAGGGGTGGCCGAAATACCGAAATTTCGGTCCAAAGTTTTGTGAACTTTTTAATAAATTTTGACTAAATTTGAACAAAATATTACCAAATTCAC[C/G]
AAAAAATGAAAAAAAAAATTTAAAATTTCGGCCAAAATTATATCGTATCGGGGGGTCCGATAGAACTGAACATTTGGATATTTCGATCCGAAATTAACTG

Reverse complement sequence

CAGTTAATTTCGGATCGAAATATCCAAATGTTCAGTTCTATCGGACCCCCCGATACGATATAATTTTGGCCGAAATTTTAAATTTTTTTTTTCATTTTTT[G/C]
GTGAATTTGGTAATATTTTGTTCAAATTTAGTCAAAATTTATTAAAAAGTTCACAAAACTTTGGACCGAAATTTCGGTATTTCGGCCACCCCTATCGTAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.40% 45.20% 0.32% 0.00% NA
All Indica  2759 46.80% 53.10% 0.14% 0.00% NA
All Japonica  1512 72.30% 27.00% 0.73% 0.00% NA
Aus  269 11.50% 88.50% 0.00% 0.00% NA
Indica I  595 52.10% 47.90% 0.00% 0.00% NA
Indica II  465 39.60% 60.20% 0.22% 0.00% NA
Indica III  913 45.30% 54.70% 0.00% 0.00% NA
Indica Intermediate  786 48.70% 50.90% 0.38% 0.00% NA
Temperate Japonica  767 71.80% 27.10% 1.04% 0.00% NA
Tropical Japonica  504 74.00% 26.00% 0.00% 0.00% NA
Japonica Intermediate  241 70.10% 28.60% 1.24% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 72.20% 27.80% 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
vg1126391061 C -> G LOC_Os11g43710.1 downstream_gene_variant ; 2625.0bp to feature; MODIFIER silent_mutation Average:37.839; most accessible tissue: Callus, score: 67.989 N N N N
vg1126391061 C -> G LOC_Os11g43700-LOC_Os11g43710 intergenic_region ; MODIFIER silent_mutation Average:37.839; most accessible tissue: Callus, score: 67.989 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126391061 NA 1.50E-06 mr1191 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
vg1126391061 NA 5.97E-09 mr1644 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
vg1126391061 1.80E-06 NA mr1696 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
vg1126391061 7.38E-06 NA mr1696 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
vg1126391061 NA 9.07E-11 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