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Detailed information for vg1119461292:

Variant ID: vg1119461292 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19461292
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCGCTTCCGCTTGCGTTAAAATATTTTCCATGTGCGTCGAAAAAAAATTATGTATATCGTTGCTCAGAAATCCATGCACATGTTATCGCATGGGTCATT[T/C]
GGGGATGACTAGGGATCGGTCGCCCGATCCAAATCTTTAAAAATCGGCATGACGTCAACGCCGATTTACGTGTAAAACAAATTCAAACTGATTTTTCTCT

Reverse complement sequence

AGAGAAAAATCAGTTTGAATTTGTTTTACACGTAAATCGGCGTTGACGTCATGCCGATTTTTAAAGATTTGGATCGGGCGACCGATCCCTAGTCATCCCC[A/G]
AATGACCCATGCGATAACATGTGCATGGATTTCTGAGCAACGATATACATAATTTTTTTTCGACGCACATGGAAAATATTTTAACGCAAGCGGAAGCGAA

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 59.40% 31.90% 0.00% 8.74% NA
All Indica  2759 90.20% 1.20% 0.00% 8.59% NA
All Japonica  1512 6.10% 90.70% 0.00% 3.17% NA
Aus  269 56.50% 1.50% 0.00% 42.01% NA
Indica I  595 92.30% 1.70% 0.00% 6.05% NA
Indica II  465 77.00% 0.60% 0.00% 22.37% NA
Indica III  913 96.50% 0.40% 0.00% 3.07% NA
Indica Intermediate  786 89.10% 2.20% 0.00% 8.78% NA
Temperate Japonica  767 3.70% 94.00% 0.00% 2.35% NA
Tropical Japonica  504 10.90% 87.70% 0.00% 1.39% NA
Japonica Intermediate  241 3.70% 86.70% 0.00% 9.54% NA
VI/Aromatic  96 31.20% 68.80% 0.00% 0.00% NA
Intermediate  90 47.80% 35.60% 0.00% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1119461292 T -> DEL N N silent_mutation Average:38.766; most accessible tissue: Callus, score: 93.081 N N N N
vg1119461292 T -> C LOC_Os11g32940-LOC_Os11g32950 intergenic_region ; MODIFIER silent_mutation Average:38.766; most accessible tissue: Callus, score: 93.081 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119461292 NA 6.68E-10 mr1097 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
vg1119461292 NA 1.82E-19 mr1133 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
vg1119461292 NA 3.76E-09 mr1198 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
vg1119461292 NA 4.13E-12 mr1205 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
vg1119461292 NA 7.01E-06 mr1231 Jap_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
vg1119461292 NA 3.25E-14 mr1376 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
vg1119461292 NA 3.25E-14 mr1431 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
vg1119461292 NA 2.77E-12 mr1667 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
vg1119461292 NA 2.19E-37 mr1670 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
vg1119461292 NA 3.36E-08 mr1680 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
vg1119461292 NA 1.44E-10 mr1683 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
vg1119461292 NA 1.01E-23 mr1698 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
vg1119461292 NA 5.14E-20 mr1767 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
vg1119461292 NA 2.06E-15 mr1950 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
vg1119461292 NA 2.14E-07 mr1979 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
vg1119461292 NA 9.12E-16 mr1133_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
vg1119461292 NA 1.43E-10 mr1667_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
vg1119461292 NA 5.84E-23 mr1698_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