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Detailed information for vg1124078197:

Variant ID: vg1124078197 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24078197
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACGGTTACGAACTCGACACCGGATTTGAGGTCCTCGGCAAGAGCTGCTGCGTCAGAACTGGGAGCAATGTGCACAAGCAAGTGAACCCACACATCAGA[T/A]
AGGATCTCCCAACGACATTTTTGGTCCTCCTTCTTGATGAGTTCATTAGCCAGTATAGCACCTTGTTGCAATATGTTTCCACTCAGATTTAGACCATGCG

Reverse complement sequence

CGCATGGTCTAAATCTGAGTGGAAACATATTGCAACAAGGTGCTATACTGGCTAATGAACTCATCAAGAAGGAGGACCAAAAATGTCGTTGGGAGATCCT[A/T]
TCTGATGTGTGGGTTCACTTGCTTGTGCACATTGCTCCCAGTTCTGACGCAGCAGCTCTTGCCGAGGACCTCAAATCCGGTGTCGAGTTCGTAACCGTCA

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 37.70% 17.80% 0.72% 43.78% NA
All Indica  2759 32.80% 3.00% 1.05% 63.14% NA
All Japonica  1512 45.80% 40.50% 0.20% 13.49% NA
Aus  269 23.40% 44.60% 0.74% 31.23% NA
Indica I  595 4.90% 3.20% 0.84% 91.09% NA
Indica II  465 26.90% 2.20% 0.43% 70.54% NA
Indica III  913 54.90% 1.00% 0.88% 43.26% NA
Indica Intermediate  786 31.90% 5.60% 1.78% 60.69% NA
Temperate Japonica  767 39.20% 52.90% 0.26% 7.56% NA
Tropical Japonica  504 52.60% 33.50% 0.00% 13.89% NA
Japonica Intermediate  241 52.70% 15.40% 0.41% 31.54% NA
VI/Aromatic  96 86.50% 1.00% 0.00% 12.50% NA
Intermediate  90 42.20% 27.80% 0.00% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1124078197 T -> A LOC_Os11g40390.1 synonymous_variant ; p.Leu333Leu; LOW synonymous_codon Average:19.417; most accessible tissue: Callus, score: 82.607 N N N N
vg1124078197 T -> DEL LOC_Os11g40390.1 N frameshift_variant Average:19.417; most accessible tissue: Callus, score: 82.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124078197 NA 7.70E-06 mr1050_2 Ind_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
vg1124078197 6.94E-06 NA mr1088_2 Ind_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
vg1124078197 7.12E-06 NA mr1199_2 Ind_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
vg1124078197 3.22E-06 NA mr1246_2 Ind_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
vg1124078197 7.13E-06 3.36E-06 mr1272_2 Ind_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
vg1124078197 7.38E-06 4.28E-06 mr1595_2 Ind_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
vg1124078197 NA 3.19E-06 mr1600_2 Ind_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
vg1124078197 1.95E-06 2.88E-06 mr1607_2 Ind_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
vg1124078197 8.72E-06 NA mr1763_2 Ind_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
vg1124078197 1.85E-06 1.85E-06 mr1852_2 Ind_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
vg1124078197 NA 5.53E-06 mr1888_2 Ind_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
vg1124078197 5.64E-06 NA mr1909_2 Ind_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