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Detailed information for vg0604778086:

Variant ID: vg0604778086 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4778086
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


GTACCTTTTTCCTCCCCTAATGCAAGCTGGTGGTTCCTTTGGTATATATCTTGATTCTTGAGGTATCTCTACTCTTCTATGTATGATGAAGATTTGGTTG[C/T]
GCTTTAATTGGATCTGTTCCCATAATTGTACAAATCAGGGGTAGCTGCACCAACACATGGTTTACAATTACACTTAATAAGTGTCACGCCCCGAACTAGT

Reverse complement sequence

ACTAGTTCGGGGCGTGACACTTATTAAGTGTAATTGTAAACCATGTGTTGGTGCAGCTACCCCTGATTTGTACAATTATGGGAACAGATCCAATTAAAGC[G/A]
CAACCAAATCTTCATCATACATAGAAGAGTAGAGATACCTCAAGAATCAAGATATATACCAAAGGAACCACCAGCTTGCATTAGGGGAGGAAAAAGGTAC

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 88.60% 8.20% 3.15% 0.00% NA
All Indica  2759 80.80% 13.80% 5.36% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 60.70% 24.00% 15.29% 0.00% NA
Indica II  465 95.10% 3.90% 1.08% 0.00% NA
Indica III  913 88.30% 11.10% 0.66% 0.00% NA
Indica Intermediate  786 79.00% 15.10% 5.85% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 6.70% 1.11% 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
vg0604778086 C -> T LOC_Os06g09420-LOC_Os06g09430 intergenic_region ; MODIFIER silent_mutation Average:34.436; most accessible tissue: Zhenshan97 flower, score: 55.587 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604778086 4.38E-06 1.23E-11 mr1201 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
vg0604778086 NA 2.59E-12 mr1201 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
vg0604778086 NA 7.22E-09 mr1219 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
vg0604778086 NA 9.25E-11 mr1219 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
vg0604778086 9.11E-07 3.06E-14 mr1274 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
vg0604778086 7.35E-06 2.89E-12 mr1274 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
vg0604778086 NA 6.06E-10 mr1201_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
vg0604778086 NA 4.35E-10 mr1201_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
vg0604778086 NA 2.14E-07 mr1219_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
vg0604778086 NA 3.29E-09 mr1219_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
vg0604778086 NA 8.24E-12 mr1274_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
vg0604778086 NA 1.15E-11 mr1274_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