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Detailed information for vg1119207316:

Variant ID: vg1119207316 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19207316
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GATAAGCACTTGCTGAACATCTTTATATTCCCTCCTAAGTTTTTTTCAGTTCACAGTTGCTTAGTTCCCTGTCTCACGTATATTTATAGACAACGTTCCG[C/T]
ATCAAACGTGCGGTGTATCATCTAGTATATACATGTATTTCAAAGTTCTCAAATATTTTATTAGACCTCATGTTTCAAAAATGTATCCTCTCGTTTGTAC

Reverse complement sequence

GTACAAACGAGAGGATACATTTTTGAAACATGAGGTCTAATAAAATATTTGAGAACTTTGAAATACATGTATATACTAGATGATACACCGCACGTTTGAT[G/A]
CGGAACGTTGTCTATAAATATACGTGAGACAGGGAACTAAGCAACTGTGAACTGAAAAAAACTTAGGAGGGAATATAAAGATGTTCAGCAAGTGCTTATC

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 48.80% 26.00% 3.87% 21.31% NA
All Indica  2759 28.50% 41.00% 4.20% 26.28% NA
All Japonica  1512 91.60% 1.60% 0.20% 6.61% NA
Aus  269 3.70% 17.80% 18.22% 60.22% NA
Indica I  595 63.90% 3.40% 1.34% 31.43% NA
Indica II  465 24.70% 61.90% 6.24% 7.10% NA
Indica III  913 10.10% 54.00% 3.29% 32.64% NA
Indica Intermediate  786 25.30% 42.10% 6.23% 26.34% NA
Temperate Japonica  767 96.10% 1.20% 0.00% 2.74% NA
Tropical Japonica  504 87.30% 2.40% 0.40% 9.92% NA
Japonica Intermediate  241 86.30% 1.20% 0.41% 12.03% NA
VI/Aromatic  96 80.20% 2.10% 10.42% 7.29% NA
Intermediate  90 53.30% 26.70% 5.56% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1119207316 C -> T LOC_Os11g32540.1 downstream_gene_variant ; 381.0bp to feature; MODIFIER silent_mutation Average:43.155; most accessible tissue: Callus, score: 70.187 N N N N
vg1119207316 C -> T LOC_Os11g32550.1 downstream_gene_variant ; 3926.0bp to feature; MODIFIER silent_mutation Average:43.155; most accessible tissue: Callus, score: 70.187 N N N N
vg1119207316 C -> T LOC_Os11g32530-LOC_Os11g32540 intergenic_region ; MODIFIER silent_mutation Average:43.155; most accessible tissue: Callus, score: 70.187 N N N N
vg1119207316 C -> DEL N N silent_mutation Average:43.155; most accessible tissue: Callus, score: 70.187 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119207316 NA 1.21E-06 mr1030 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
vg1119207316 NA 4.99E-06 mr1050 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
vg1119207316 NA 1.65E-06 mr1064 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
vg1119207316 NA 6.63E-07 mr1272 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
vg1119207316 NA 2.58E-06 mr1432 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
vg1119207316 NA 1.20E-06 mr1531 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
vg1119207316 NA 3.66E-06 mr1614 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
vg1119207316 NA 1.56E-06 mr1629 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
vg1119207316 NA 4.38E-09 mr1668 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
vg1119207316 NA 3.20E-06 mr1749 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
vg1119207316 NA 1.20E-07 mr1928 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
vg1119207316 NA 6.64E-09 mr1958 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
vg1119207316 NA 8.60E-06 mr1958 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
vg1119207316 NA 4.68E-06 mr1974 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
vg1119207316 NA 3.95E-06 mr1974 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
vg1119207316 NA 2.74E-06 mr1984 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