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Detailed information for vg0420166000:

Variant ID: vg0420166000 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20166000
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTCTTTTTCTTTTTAAGTGGGCCGATTCACAGACAAGCAACCAAGTAGGATGATTCAATCCTAACTTGATGTCAAGGACGAACCCTAAAATATCATC[A/G]
CAAGAAAAATGACGGCTCTCATTTTTACTTGGGATTGATTTTTCCTTGTACAGCCAATTGTATTCTCTCTGTCTCGGTGCTGAAATTGAGCCTAACATAC

Reverse complement sequence

GTATGTTAGGCTCAATTTCAGCACCGAGACAGAGAGAATACAATTGGCTGTACAAGGAAAAATCAATCCCAAGTAAAAATGAGAGCCGTCATTTTTCTTG[T/C]
GATGATATTTTAGGGTTCGTCCTTGACATCAAGTTAGGATTGAATCATCCTACTTGGTTGCTTGTCTGTGAATCGGCCCACTTAAAAAGAAAAAGAAAAT

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 93.90% 6.10% 0.00% 0.00% NA
All Indica  2759 93.90% 6.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 62.10% 37.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 85.20% 14.80% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 4.10% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0420166000 A -> G LOC_Os04g33320.1 upstream_gene_variant ; 4550.0bp to feature; MODIFIER silent_mutation Average:38.474; most accessible tissue: Callus, score: 70.832 N N N N
vg0420166000 A -> G LOC_Os04g33390.1 upstream_gene_variant ; 3585.0bp to feature; MODIFIER silent_mutation Average:38.474; most accessible tissue: Callus, score: 70.832 N N N N
vg0420166000 A -> G LOC_Os04g33320-LOC_Os04g33390 intergenic_region ; MODIFIER silent_mutation Average:38.474; most accessible tissue: Callus, score: 70.832 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420166000 1.90E-07 3.54E-09 mr1392 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
vg0420166000 NA 6.71E-06 mr1393 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
vg0420166000 NA 1.92E-10 mr1722 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