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Detailed information for vg0434912939:

Variant ID: vg0434912939 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34912939
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.03, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CTGGCCTGCCTGTCGTTCTTCCTTTTAATCATCATTAGTGTTCTATTTGGTGTTTTATTAACAGTTTTTATATGTCGTATCAACCGCCACCACTCTACTC[T/C]
TTTATAGGCTTGTTACTTAAATTATCTCGTCATGTGTTTTAGATGGTTTTTTCTTTCGATAGTCTTTATTTTTATCACATTTTTCAGTTATTTATAAATT

Reverse complement sequence

AATTTATAAATAACTGAAAAATGTGATAAAAATAAAGACTATCGAAAGAAAAAACCATCTAAAACACATGACGAGATAATTTAAGTAACAAGCCTATAAA[A/G]
GAGTAGAGTGGTGGCGGTTGATACGACATATAAAAACTGTTAATAAAACACCAAATAGAACACTAATGATGATTAAAAGGAAGAACGACAGGCAGGCCAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.70% 14.30% 0.99% 0.00% NA
All Indica  2759 81.40% 17.00% 1.67% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 37.90% 62.10% 0.00% 0.00% NA
Indica I  595 97.00% 2.20% 0.84% 0.00% NA
Indica II  465 52.30% 46.20% 1.51% 0.00% NA
Indica III  913 87.10% 11.30% 1.64% 0.00% NA
Indica Intermediate  786 80.20% 17.40% 2.42% 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% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 1.11% 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
vg0434912939 T -> C LOC_Os04g58710.1 upstream_gene_variant ; 2278.0bp to feature; MODIFIER silent_mutation Average:32.518; most accessible tissue: Minghui63 root, score: 50.524 N N N N
vg0434912939 T -> C LOC_Os04g58720.1 upstream_gene_variant ; 2852.0bp to feature; MODIFIER silent_mutation Average:32.518; most accessible tissue: Minghui63 root, score: 50.524 N N N N
vg0434912939 T -> C LOC_Os04g58710-LOC_Os04g58720 intergenic_region ; MODIFIER silent_mutation Average:32.518; most accessible tissue: Minghui63 root, score: 50.524 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434912939 NA 2.58E-06 mr1075 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
vg0434912939 NA 5.89E-06 mr1149 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
vg0434912939 NA 1.18E-06 mr1441 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
vg0434912939 NA 1.40E-12 mr1565 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