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Detailed information for vg0221167643:

Variant ID: vg0221167643 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21167643
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.06, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TAGTTTAAAGCACTCACAATGAAGTTAGCTTGCAACATATGGTTGAAGAGATAATATCCGCCAAAAAAAGGTTCATTGCATCATACACCTTGACGTAGGG[A/G]
GATTAGTCTGTTCCTTTGTATAATAATTCATCTTTCGCTTTGGAGGTTTGAAATCTTGATAATAACTTCAAAAATGACTAGCTTTTCATTATTTCATCCA

Reverse complement sequence

TGGATGAAATAATGAAAAGCTAGTCATTTTTGAAGTTATTATCAAGATTTCAAACCTCCAAAGCGAAAGATGAATTATTATACAAAGGAACAGACTAATC[T/C]
CCCTACGTCAAGGTGTATGATGCAATGAACCTTTTTTTGGCGGATATTATCTCTTCAACCATATGTTGCAAGCTAACTTCATTGTGAGTGCTTTAAACTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.10% 40.70% 0.08% 0.06% NA
All Indica  2759 95.30% 4.50% 0.14% 0.11% NA
All Japonica  1512 1.60% 98.40% 0.00% 0.00% NA
Aus  269 27.90% 72.10% 0.00% 0.00% NA
Indica I  595 99.20% 0.50% 0.34% 0.00% NA
Indica II  465 97.20% 2.60% 0.00% 0.22% NA
Indica III  913 94.60% 5.30% 0.00% 0.11% NA
Indica Intermediate  786 92.00% 7.60% 0.25% 0.13% NA
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 30.20% 69.80% 0.00% 0.00% NA
Intermediate  90 42.20% 57.80% 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
vg0221167643 A -> G LOC_Os02g35200.1 downstream_gene_variant ; 1957.0bp to feature; MODIFIER silent_mutation Average:54.977; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N
vg0221167643 A -> G LOC_Os02g35220.1 downstream_gene_variant ; 2886.0bp to feature; MODIFIER silent_mutation Average:54.977; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N
vg0221167643 A -> G LOC_Os02g35210.1 intron_variant ; MODIFIER silent_mutation Average:54.977; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N
vg0221167643 A -> DEL N N silent_mutation Average:54.977; most accessible tissue: Minghui63 flag leaf, score: 73.752 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221167643 NA 1.47E-54 mr1109 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
vg0221167643 NA 2.03E-32 mr1129 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
vg0221167643 NA 4.79E-43 mr1144 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
vg0221167643 NA 4.25E-15 mr1164 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
vg0221167643 NA 5.62E-31 mr1243 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
vg0221167643 NA 2.34E-26 mr1251 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
vg0221167643 NA 3.97E-19 mr1255 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
vg0221167643 NA 3.90E-32 mr1257 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
vg0221167643 NA 1.87E-36 mr1435 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
vg0221167643 NA 1.31E-25 mr1551 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
vg0221167643 NA 5.12E-11 mr1720 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
vg0221167643 NA 1.46E-06 mr1756 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
vg0221167643 NA 4.53E-28 mr1793 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
vg0221167643 NA 5.08E-32 mr1037_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
vg0221167643 NA 1.61E-44 mr1094_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
vg0221167643 NA 5.39E-64 mr1109_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
vg0221167643 NA 1.99E-36 mr1129_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
vg0221167643 NA 1.71E-35 mr1257_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
vg0221167643 NA 1.29E-15 mr1720_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