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Detailed information for vg0221873638:

Variant ID: vg0221873638 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21873638
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGCGAGGTGGACCCGGCCCACCGGTTCCCCTCCCTCTCTCCCCGCGCGTGCCTTTGGGCCGCCTTCTCGGGCCGGCCGGCCCATTTAGCTCGGCCGAGC[C/T]
GCCCTTTTCTCTCGGGCCGCACCCTAGCCGCCTGAGGGAAGTCTATTTCCCCTCCCTCTTTCTTTTCTTTTTTCAAAAGGGTTTAATTAAATCCTTTTTC

Reverse complement sequence

GAAAAAGGATTTAATTAAACCCTTTTGAAAAAAGAAAAGAAAGAGGGAGGGGAAATAGACTTCCCTCAGGCGGCTAGGGTGCGGCCCGAGAGAAAAGGGC[G/A]
GCTCGGCCGAGCTAAATGGGCCGGCCGGCCCGAGAAGGCGGCCCAAAGGCACGCGCGGGGAGAGAGGGAGGGGAACCGGTGGGCCGGGTCCACCTCGCGT

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 66.10% 33.70% 0.15% 0.00% NA
All Indica  2759 97.50% 2.40% 0.07% 0.00% NA
All Japonica  1512 7.90% 92.00% 0.07% 0.00% NA
Aus  269 98.90% 0.70% 0.37% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 98.10% 1.80% 0.11% 0.00% NA
Indica Intermediate  786 95.30% 4.60% 0.13% 0.00% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 19.40% 80.60% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 94.20% 0.41% 0.00% NA
VI/Aromatic  96 8.30% 90.60% 1.04% 0.00% NA
Intermediate  90 46.70% 51.10% 2.22% 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
vg0221873638 C -> T LOC_Os02g36230.1 downstream_gene_variant ; 4058.0bp to feature; MODIFIER silent_mutation Average:32.08; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N
vg0221873638 C -> T LOC_Os02g36230-LOC_Os02g36250 intergenic_region ; MODIFIER silent_mutation Average:32.08; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221873638 NA 6.87E-07 mr1305 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
vg0221873638 NA 2.22E-06 mr1586 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
vg0221873638 NA 9.71E-11 mr1714 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
vg0221873638 NA 3.53E-06 mr1246_2 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
vg0221873638 4.97E-06 6.44E-07 mr1305_2 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
vg0221873638 NA 2.39E-16 mr1592_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
vg0221873638 NA 1.93E-10 mr1595_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
vg0221873638 NA 5.49E-09 mr1600_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
vg0221873638 NA 1.24E-06 mr1691_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
vg0221873638 NA 4.05E-08 mr1783_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
vg0221873638 NA 2.56E-09 mr1947_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