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Detailed information for vg0720359934:

Variant ID: vg0720359934 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20359934
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, T: 0.21, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:


TCGAGATACACGAAGTTTGATCACTCTTATGATAAATAAATAATGTAAACGAAGTGAGTGTAGCTTAACTGGTTAGGTTCTTTGTAATGGAACCAGCCTA[C/T]
CCGAGTTCAAATTTTAGATTTGACACGGGTGCTCGCAGAGTGTTTGTATTTATTGTTAATTATTCTTTCAACGGTAGGCGAACGAGCCATTTATGATGGA

Reverse complement sequence

TCCATCATAAATGGCTCGTTCGCCTACCGTTGAAAGAATAATTAACAATAAATACAAACACTCTGCGAGCACCCGTGTCAAATCTAAAATTTGAACTCGG[G/A]
TAGGCTGGTTCCATTACAAAGAACCTAACCAGTTAAGCTACACTCACTTCGTTTACATTATTTATTTATCATAAGAGTGATCAAACTTCGTGTATCTCGA

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 66.90% 33.00% 0.06% 0.00% NA
All Indica  2759 88.70% 11.20% 0.04% 0.00% NA
All Japonica  1512 27.40% 72.50% 0.07% 0.00% NA
Aus  269 90.00% 9.70% 0.37% 0.00% NA
Indica I  595 89.40% 10.60% 0.00% 0.00% NA
Indica II  465 84.50% 15.30% 0.22% 0.00% NA
Indica III  913 95.40% 4.60% 0.00% 0.00% NA
Indica Intermediate  786 83.00% 17.00% 0.00% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 65.90% 33.90% 0.20% 0.00% NA
Japonica Intermediate  241 24.90% 75.10% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 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
vg0720359934 C -> T LOC_Os07g34060-LOC_Os07g34070 intergenic_region ; MODIFIER silent_mutation Average:48.277; most accessible tissue: Callus, score: 69.339 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720359934 NA 2.58E-08 mr1248 Jap_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
vg0720359934 NA 5.15E-08 mr1364 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
vg0720359934 NA 6.89E-07 mr1364 Jap_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
vg0720359934 NA 1.31E-08 mr1443 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
vg0720359934 NA 1.36E-07 mr1443 Jap_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
vg0720359934 NA 1.64E-09 mr1563 Jap_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
vg0720359934 NA 1.07E-06 mr1629 Jap_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
vg0720359934 NA 2.71E-16 mr1699 Jap_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
vg0720359934 NA 2.69E-12 mr1364_2 Jap_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
vg0720359934 NA 1.51E-07 mr1533_2 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
vg0720359934 NA 4.23E-09 mr1563_2 Jap_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