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Detailed information for vg0332502161:

Variant ID: vg0332502161 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 32502161
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TTATATATACTCCCTTCATCCTTAAATGTTTGACGCCGTTGACTTTTTTAAATATGTTTGACCGTTTGTCTTATTCAAAAAATTTAAGCAATTATTAATT[C/T,A]
TTTTCCTACCATTTAATTTATTGTTAAATATACTTTTATGTATACATATAGTTTTACATATTTCACAAAAGTTTTTTGAATAAGACGAACGGCCAAACAT

Reverse complement sequence

ATGTTTGGCCGTTCGTCTTATTCAAAAAACTTTTGTGAAATATGTAAAACTATATGTATACATAAAAGTATATTTAACAATAAATTAAATGGTAGGAAAA[G/A,T]
AATTAATAATTGCTTAAATTTTTTGAATAAGACAAACGGTCAAACATATTTAAAAAAGTCAACGGCGTCAAACATTTAAGGATGAAGGGAGTATATATAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.60% 8.00% 0.34% 0.00% A: 0.02%
All Indica  2759 86.20% 13.20% 0.54% 0.00% NA
All Japonica  1512 99.50% 0.40% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 90.60% 9.20% 0.17% 0.00% NA
Indica II  465 88.00% 11.20% 0.86% 0.00% NA
Indica III  913 86.30% 13.40% 0.33% 0.00% NA
Indica Intermediate  786 81.80% 17.30% 0.89% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 0.00% A: 1.04%
Intermediate  90 90.00% 10.00% 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
vg0332502161 C -> T LOC_Os03g57020-LOC_Os03g57030 intergenic_region ; MODIFIER silent_mutation Average:25.3; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0332502161 C -> A LOC_Os03g57020-LOC_Os03g57030 intergenic_region ; MODIFIER silent_mutation Average:25.3; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0332502161 2.40E-07 NA mr1723 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
vg0332502161 1.49E-07 1.64E-09 mr1723 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
vg0332502161 NA 1.19E-06 mr1734 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
vg0332502161 4.05E-08 NA mr1723_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
vg0332502161 7.96E-08 4.00E-13 mr1723_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