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Detailed information for vg0321774470:

Variant ID: vg0321774470 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21774470
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.59, C: 0.41, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


CGGGATCTGCGAACACCCAACCCAACCGACGCCGTTGCCTCCGCCGCTCCGAGCCTCCGATCCATTGCTGCGAGAAGGCTATTGGGTGATCAGCGCACGT[T/C]
CCTCCCCGCACGACTGGACACGTGTCGCGCGCGGAGCATAGTGGAAAAAACCGGACCGGTCCGGCGGTTGAACCAAAAAACCGGAACCGACATGCATTCG

Reverse complement sequence

CGAATGCATGTCGGTTCCGGTTTTTTGGTTCAACCGCCGGACCGGTCCGGTTTTTTCCACTATGCTCCGCGCGCGACACGTGTCCAGTCGTGCGGGGAGG[A/G]
ACGTGCGCTGATCACCCAATAGCCTTCTCGCAGCAATGGATCGGAGGCTCGGAGCGGCGGAGGCAACGGCGTCGGTTGGGTTGGGTGTTCGCAGATCCCG

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 52.50% 47.20% 0.25% 0.08% NA
All Indica  2759 34.40% 65.00% 0.43% 0.14% NA
All Japonica  1512 97.90% 2.10% 0.00% 0.00% NA
Aus  269 0.00% 100.00% 0.00% 0.00% NA
Indica I  595 75.00% 24.90% 0.17% 0.00% NA
Indica II  465 14.00% 84.70% 1.08% 0.22% NA
Indica III  913 27.60% 71.60% 0.44% 0.33% NA
Indica Intermediate  786 23.80% 76.00% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 5.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 53.30% 46.70% 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
vg0321774470 T -> C LOC_Os03g39210.1 downstream_gene_variant ; 861.0bp to feature; MODIFIER silent_mutation Average:76.74; most accessible tissue: Callus, score: 92.484 N N N N
vg0321774470 T -> C LOC_Os03g39200-LOC_Os03g39210 intergenic_region ; MODIFIER silent_mutation Average:76.74; most accessible tissue: Callus, score: 92.484 N N N N
vg0321774470 T -> DEL N N silent_mutation Average:76.74; most accessible tissue: Callus, score: 92.484 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321774470 NA 8.93E-06 mr1029 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
vg0321774470 NA 1.45E-06 mr1074 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
vg0321774470 NA 1.30E-06 mr1081 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
vg0321774470 NA 2.87E-08 mr1130 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
vg0321774470 NA 1.18E-07 mr1148 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
vg0321774470 NA 2.51E-09 mr1193 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
vg0321774470 NA 9.13E-09 mr1221 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
vg0321774470 NA 2.17E-07 mr1254 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
vg0321774470 NA 4.57E-06 mr1291 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
vg0321774470 NA 8.42E-09 mr1637 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
vg0321774470 NA 1.46E-06 mr1803 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
vg0321774470 7.44E-06 NA mr1857 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
vg0321774470 NA 4.50E-09 mr1857 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
vg0321774470 NA 9.55E-06 mr1868 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
vg0321774470 NA 1.54E-06 mr1928 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
vg0321774470 NA 9.42E-18 mr1715_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