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Detailed information for vg0406728056:

Variant ID: vg0406728056 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6728056
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTAATGGTTCTCATTCGAAATTTATTCCAGTGTTATTAGTACTGTACATCCATTACTGTACTAATGGCTCATTTTACCAGCAAAAGTTTTACAATATTG[C/T]
TTTACTTAATCTTGCTGCAACAAAAATAAATTTAGCATGTTGATTTTATAACTTTCTTTCATTTCTTTTGAAATCTGTTATTCAAAAGTATAAAATTTGT

Reverse complement sequence

ACAAATTTTATACTTTTGAATAACAGATTTCAAAAGAAATGAAAGAAAGTTATAAAATCAACATGCTAAATTTATTTTTGTTGCAGCAAGATTAAGTAAA[G/A]
CAATATTGTAAAACTTTTGCTGGTAAAATGAGCCATTAGTACAGTAATGGATGTACAGTACTAATAACACTGGAATAAATTTCGAATGAGAACCATTAAA

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 45.30% 0.40% 34.85% 19.45% NA
All Indica  2759 19.90% 0.50% 50.27% 29.32% NA
All Japonica  1512 96.40% 0.10% 1.19% 2.38% NA
Aus  269 17.80% 1.50% 65.06% 15.61% NA
Indica I  595 15.10% 0.20% 30.08% 54.62% NA
Indica II  465 23.40% 0.90% 48.39% 27.31% NA
Indica III  913 21.60% 0.80% 64.84% 12.81% NA
Indica Intermediate  786 19.30% 0.40% 49.75% 30.53% NA
Temperate Japonica  767 97.00% 0.00% 0.13% 2.87% NA
Tropical Japonica  504 97.20% 0.20% 1.39% 1.19% NA
Japonica Intermediate  241 92.50% 0.00% 4.15% 3.32% NA
VI/Aromatic  96 39.60% 0.00% 39.58% 20.83% NA
Intermediate  90 54.40% 0.00% 32.22% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0406728056 C -> DEL N N silent_mutation Average:8.225; most accessible tissue: Callus, score: 22.59 N N N N
vg0406728056 C -> T LOC_Os04g12200-LOC_Os04g12220 intergenic_region ; MODIFIER silent_mutation Average:8.225; most accessible tissue: Callus, score: 22.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406728056 NA 9.19E-94 mr1071 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
vg0406728056 NA 7.23E-86 mr1080 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
vg0406728056 NA 1.19E-80 mr1100 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
vg0406728056 NA 2.19E-99 mr1140 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
vg0406728056 NA 2.93E-99 mr1203 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
vg0406728056 NA 1.01E-92 mr1395 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
vg0406728056 NA 3.95E-39 mr1480 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
vg0406728056 NA 1.82E-85 mr1613 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
vg0406728056 NA 9.73E-99 mr1618 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
vg0406728056 NA 3.16E-70 mr1619 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
vg0406728056 NA 1.04E-14 mr1035_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
vg0406728056 2.94E-06 1.57E-116 mr1071_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
vg0406728056 NA 1.10E-114 mr1080_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
vg0406728056 NA 4.36E-107 mr1100_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
vg0406728056 2.09E-06 1.46E-122 mr1203_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
vg0406728056 1.53E-08 4.59E-74 mr1402_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
vg0406728056 NA 7.72E-133 mr1613_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
vg0406728056 NA 4.33E-108 mr1619_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
vg0406728056 NA 2.63E-32 mr1631_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
vg0406728056 NA 1.78E-86 mr1795_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
vg0406728056 NA 3.87E-31 mr1913_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