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Detailed information for vg0139981469:

Variant ID: vg0139981469 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 39981469
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.20, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:


GCTATATATAGTAGTTATTCTAATTCACATCGAATCGGATACGAGCGACATACAACCAGCTCAAAATCTGACTCAAACACGGATGACGTTCCAAAATTTT[G/A]
GCGAAAACATCTTCAATTTTTATATTTTTATTAATTATTAATTCATATGGTAGCTTTATACTAGCTCTATAGTTTTGTGATATATCGACTTAGATATGTG

Reverse complement sequence

CACATATCTAAGTCGATATATCACAAAACTATAGAGCTAGTATAAAGCTACCATATGAATTAATAATTAATAAAAATATAAAAATTGAAGATGTTTTCGC[C/T]
AAAATTTTGGAACGTCATCCGTGTTTGAGTCAGATTTTGAGCTGGTTGTATGTCGCTCGTATCCGATTCGATGTGAATTAGAATAACTACTATATATAGC

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 62.00% 38.00% 0.06% 0.00% NA
All Indica  2759 92.70% 7.20% 0.07% 0.00% NA
All Japonica  1512 2.20% 97.80% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.20% 1.70% 0.17% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 92.80% 7.20% 0.00% 0.00% NA
Indica Intermediate  786 85.50% 14.40% 0.13% 0.00% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 2.20% 97.80% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.40% 0.41% 0.00% NA
VI/Aromatic  96 25.00% 75.00% 0.00% 0.00% NA
Intermediate  90 48.90% 51.10% 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
vg0139981469 G -> A LOC_Os01g68820.1 upstream_gene_variant ; 3754.0bp to feature; MODIFIER silent_mutation Average:48.892; most accessible tissue: Minghui63 root, score: 62.438 N N N N
vg0139981469 G -> A LOC_Os01g68810-LOC_Os01g68820 intergenic_region ; MODIFIER silent_mutation Average:48.892; most accessible tissue: Minghui63 root, score: 62.438 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0139981469 NA 8.30E-66 mr1027 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
vg0139981469 NA 1.68E-28 mr1075 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
vg0139981469 NA 4.55E-06 mr1119 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
vg0139981469 1.29E-06 NA mr1121 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
vg0139981469 NA 4.02E-06 mr1121 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
vg0139981469 NA 1.55E-22 mr1155 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
vg0139981469 NA 3.93E-07 mr1162 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
vg0139981469 NA 5.94E-11 mr1281 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
vg0139981469 NA 6.53E-11 mr1630 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
vg0139981469 NA 7.35E-23 mr1888 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
vg0139981469 NA 2.56E-11 mr1902 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
vg0139981469 NA 1.16E-36 mr1155_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
vg0139981469 NA 6.10E-11 mr1216_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
vg0139981469 NA 1.64E-06 mr1533_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