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Detailed information for vg0321991817:

Variant ID: vg0321991817 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21991817
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CAGAAGTTCTAACAGACTGTCGAAACTGGTATTAGACCATCCATGTCTCGCCTTTAACCTCATAAGTTCAAGAACTGACCGTAGTGTTGTGAACTCACTG[T/C]
CACAGCCCTTCGACTCATCGTACAAAACTTCCTTAGCTTCCTGTAAAGCTTCAAAGTTATTTAAACCTCTAGCTGACCCCATCAGCACCTCGGGTTCTGC

Reverse complement sequence

GCAGAACCCGAGGTGCTGATGGGGTCAGCTAGAGGTTTAAATAACTTTGAAGCTTTACAGGAAGCTAAGGAAGTTTTGTACGATGAGTCGAAGGGCTGTG[A/G]
CAGTGAGTTCACAACACTACGGTCAGTTCTTGAACTTATGAGGTTAAAGGCGAGACATGGATGGTCTAATACCAGTTTCGACAGTCTGTTAGAACTTCTG

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 64.10% 35.60% 0.30% 0.00% NA
All Indica  2759 41.70% 57.80% 0.51% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 80.30% 19.70% 0.00% 0.00% NA
Indica I  595 80.70% 18.80% 0.50% 0.00% NA
Indica II  465 16.30% 83.00% 0.65% 0.00% NA
Indica III  913 35.00% 64.60% 0.33% 0.00% NA
Indica Intermediate  786 35.00% 64.40% 0.64% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 72.20% 27.80% 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
vg0321991817 T -> C LOC_Os03g39598.1 missense_variant ; p.Asp158Gly; MODERATE nonsynonymous_codon ; D158G Average:23.016; most accessible tissue: Callus, score: 40.624 benign 1.499 TOLERATED 0.15

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321991817 1.49E-06 1.49E-06 mr1303 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
vg0321991817 6.01E-06 6.30E-06 mr1830 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