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Detailed information for vg0621044029:

Variant ID: vg0621044029 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 21044029
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTCTTATATTTTGAGACGAGGGGAGTAATAACATGAAAATGGTCACAAACTTTAATCACTTTTTGATATTAAGTTCTACTCCCTGTCATGATTCGTTGT[C/T]
CTAGGAAATGTCCCATCCATGTCAAGGTTGGGCTTTTTTTTAGACGGAGGGAGTAGTTGATTGATTGAGTTAAGTTTCGTGCAACTAAAATATTACTCCC

Reverse complement sequence

GGGAGTAATATTTTAGTTGCACGAAACTTAACTCAATCAATCAACTACTCCCTCCGTCTAAAAAAAAGCCCAACCTTGACATGGATGGGACATTTCCTAG[G/A]
ACAACGAATCATGACAGGGAGTAGAACTTAATATCAAAAAGTGATTAAAGTTTGTGACCATTTTCATGTTATTACTCCCCTCGTCTCAAAATATAAGAGA

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 94.30% 3.80% 1.84% 0.00% NA
All Indica  2759 90.40% 6.60% 3.04% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.10% 4.40% 7.56% 0.00% NA
Indica II  465 97.80% 1.30% 0.86% 0.00% NA
Indica III  913 89.90% 9.50% 0.55% 0.00% NA
Indica Intermediate  786 88.30% 7.90% 3.82% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0621044029 C -> T LOC_Os06g36000.1 downstream_gene_variant ; 2162.0bp to feature; MODIFIER silent_mutation Average:46.937; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0621044029 C -> T LOC_Os06g36010.1 downstream_gene_variant ; 4693.0bp to feature; MODIFIER silent_mutation Average:46.937; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N
vg0621044029 C -> T LOC_Os06g36000-LOC_Os06g36010 intergenic_region ; MODIFIER silent_mutation Average:46.937; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0621044029 NA 3.79E-06 mr1585 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
vg0621044029 NA 2.80E-07 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
vg0621044029 6.62E-06 2.07E-08 mr1706 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
vg0621044029 NA 2.23E-07 mr1739 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
vg0621044029 NA 4.25E-07 mr1236_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
vg0621044029 NA 1.22E-08 mr1327_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
vg0621044029 NA 1.12E-06 mr1654_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