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Detailed information for vg1111565611:

Variant ID: vg1111565611 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 11565611
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTTAAATTACTTATCGAAATCATGATCTGATTGCATCATTAAATTCGTTGCAAATAAATCTTCAAAACAAGACCACACATGGATATCCGACAAAAAAA[T/A]
TTTTTAGTTTATTATTGAATTATTTTTAAATGTTGCACGATGTTCCACCAGATATATCGGAATTGTTTCACTAAGTAGATCGAAAATGTTTCACTCGTTT

Reverse complement sequence

AAACGAGTGAAACATTTTCGATCTACTTAGTGAAACAATTCCGATATATCTGGTGGAACATCGTGCAACATTTAAAAATAATTCAATAATAAACTAAAAA[A/T]
TTTTTTTGTCGGATATCCATGTGTGGTCTTGTTTTGAAGATTTATTTGCAACGAATTTAATGATGCAATCAGATCATGATTTCGATAAGTAATTTAAGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.60% 37.70% 0.72% 0.00% NA
All Indica  2759 97.10% 2.30% 0.65% 0.00% NA
All Japonica  1512 5.80% 93.50% 0.73% 0.00% NA
Aus  269 31.20% 68.80% 0.00% 0.00% NA
Indica I  595 96.60% 1.20% 2.18% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 97.20% 2.80% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.40% 0.51% 0.00% NA
Temperate Japonica  767 3.80% 95.40% 0.78% 0.00% NA
Tropical Japonica  504 10.50% 89.10% 0.40% 0.00% NA
Japonica Intermediate  241 2.50% 96.30% 1.24% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 58.90% 35.60% 5.56% 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
vg1111565611 T -> A LOC_Os11g20070.1 downstream_gene_variant ; 4534.0bp to feature; MODIFIER silent_mutation Average:35.317; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg1111565611 T -> A LOC_Os11g20060-LOC_Os11g20070 intergenic_region ; MODIFIER silent_mutation Average:35.317; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1111565611 NA 1.03E-08 mr1047 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
vg1111565611 NA 1.12E-10 mr1336 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
vg1111565611 NA 3.95E-20 mr1580 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
vg1111565611 NA 1.15E-28 mr1793 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
vg1111565611 NA 6.99E-17 mr1825 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
vg1111565611 NA 1.76E-09 mr1198_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
vg1111565611 NA 6.51E-19 mr1218_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
vg1111565611 NA 6.05E-10 mr1228_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
vg1111565611 NA 2.47E-12 mr1325_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
vg1111565611 NA 1.50E-21 mr1401_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
vg1111565611 NA 3.68E-14 mr1579_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
vg1111565611 NA 1.45E-08 mr1751_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
vg1111565611 NA 1.57E-29 mr1825_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