Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1018076166:

Variant ID: vg1018076166 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 18076166
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCTCAATGTGATTATTCCTACTTTATTTACTCTTGATACATTTATAGCCTGCTTTTTACAAATTTCGATGTAATGATTATTTAGAAATAAATTTATATT[T/C]
GAACAAATAAGAGTGGCTAAAAATAAAACTTATTATGAAAGTAGTATATCGTACTCCTCCGTCCAAAAAAAATCCAATCCTAGCTACGAACCTGAACATA

Reverse complement sequence

TATGTTCAGGTTCGTAGCTAGGATTGGATTTTTTTTGGACGGAGGAGTACGATATACTACTTTCATAATAAGTTTTATTTTTAGCCACTCTTATTTGTTC[A/G]
AATATAAATTTATTTCTAAATAATCATTACATCGAAATTTGTAAAAAGCAGGCTATAAATGTATCAAGAGTAAATAAAGTAGGAATAATCACATTGAGAC

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 70.80% 29.20% 0.04% 0.00% NA
All Indica  2759 98.60% 1.30% 0.07% 0.00% NA
All Japonica  1512 18.30% 81.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.20% 0.25% 0.00% NA
Temperate Japonica  767 2.10% 97.90% 0.00% 0.00% NA
Tropical Japonica  504 44.80% 55.20% 0.00% 0.00% NA
Japonica Intermediate  241 14.10% 85.90% 0.00% 0.00% NA
VI/Aromatic  96 25.00% 75.00% 0.00% 0.00% NA
Intermediate  90 61.10% 38.90% 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
vg1018076166 T -> C LOC_Os10g33954.1 downstream_gene_variant ; 4523.0bp to feature; MODIFIER silent_mutation Average:30.733; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg1018076166 T -> C LOC_Os10g33950-LOC_Os10g33954 intergenic_region ; MODIFIER silent_mutation Average:30.733; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1018076166 NA 2.90E-21 mr1217 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
vg1018076166 NA 1.31E-06 mr1315 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
vg1018076166 NA 3.14E-12 mr1386 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
vg1018076166 NA 4.81E-08 mr1488 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
vg1018076166 NA 6.73E-20 mr1845 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
vg1018076166 NA 1.51E-06 mr1227_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
vg1018076166 NA 8.90E-18 mr1336_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