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Detailed information for vg0617852766:

Variant ID: vg0617852766 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17852766
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCGCCGTTGTTGGGCGTCTACGACTTCACCGCCAACCGCCTAGGTTGCTTCCACGGCTGGTGTTTTCATCGCCATTGATGGACGACTTTGTTCCTAGAT[C/T]
GACTACTTCTGCTGTCACCGAGGGAATACGACAAAGCTAAGTCATCATTTATTTTATTCTTTATATGATATTTTGCCTTTTCCTTTGCCTCACTACATCA

Reverse complement sequence

TGATGTAGTGAGGCAAAGGAAAAGGCAAAATATCATATAAAGAATAAAATAAATGATGACTTAGCTTTGTCGTATTCCCTCGGTGACAGCAGAAGTAGTC[G/A]
ATCTAGGAACAAAGTCGTCCATCAATGGCGATGAAAACACCAGCCGTGGAAGCAACCTAGGCGGTTGGCGGTGAAGTCGTAGACGCCCAACAACGGCGGC

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 87.90% 7.30% 0.30% 4.57% NA
All Indica  2759 91.00% 1.00% 0.33% 7.61% NA
All Japonica  1512 79.40% 20.30% 0.26% 0.07% NA
Aus  269 98.50% 0.00% 0.37% 1.12% NA
Indica I  595 98.20% 0.00% 0.34% 1.51% NA
Indica II  465 93.10% 2.60% 0.00% 4.30% NA
Indica III  913 85.90% 0.50% 0.33% 13.25% NA
Indica Intermediate  786 90.50% 1.40% 0.51% 7.63% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 48.00% 51.00% 0.79% 0.20% NA
Japonica Intermediate  241 84.20% 15.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 8.90% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0617852766 C -> T LOC_Os06g30780.1 upstream_gene_variant ; 4894.0bp to feature; MODIFIER silent_mutation Average:54.07; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N
vg0617852766 C -> T LOC_Os06g30780-LOC_Os06g30790 intergenic_region ; MODIFIER silent_mutation Average:54.07; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N
vg0617852766 C -> DEL N N silent_mutation Average:54.07; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617852766 NA 8.65E-24 mr1301 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
vg0617852766 NA 2.83E-15 mr1410 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
vg0617852766 NA 1.28E-07 mr1993 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
vg0617852766 2.64E-09 NA mr1033_2 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
vg0617852766 NA 2.76E-24 mr1301_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
vg0617852766 NA 1.78E-14 mr1410_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
vg0617852766 NA 1.08E-10 mr1993_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