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Detailed information for vg0301192756:

Variant ID: vg0301192756 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1192756
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TACTATGACGGCGGTCTCGCTGGTGTGATAGCGTTATTTGGTCATGCCAGTCTCGCTAGCGTGGCAACGTTATTTAGTCACGCCGCTCTTACTGATGTGG[C/T]
TGGATAAAACTGTCACGTCCATTGCATATGGCATGTTAGTGTTGTTTTATCACGTCAGGCGGGATAGTGTGACCAAAAGGTTCAAATTTTGAGAATAAGT

Reverse complement sequence

ACTTATTCTCAAAATTTGAACCTTTTGGTCACACTATCCCGCCTGACGTGATAAAACAACACTAACATGCCATATGCAATGGACGTGACAGTTTTATCCA[G/A]
CCACATCAGTAAGAGCGGCGTGACTAAATAACGTTGCCACGCTAGCGAGACTGGCATGACCAAATAACGCTATCACACCAGCGAGACCGCCGTCATAGTA

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 91.50% 8.50% 0.04% 0.00% NA
All Indica  2759 87.00% 12.90% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 89.20% 10.80% 0.00% 0.00% NA
Indica I  595 91.80% 8.20% 0.00% 0.00% NA
Indica II  465 66.00% 34.00% 0.00% 0.00% NA
Indica III  913 97.30% 2.60% 0.11% 0.00% NA
Indica Intermediate  786 83.80% 16.00% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 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 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 0.00% 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
vg0301192756 C -> T LOC_Os03g02960.1 upstream_gene_variant ; 1499.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301192756 C -> T LOC_Os03g02970.1 downstream_gene_variant ; 2319.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301192756 C -> T LOC_Os03g02939-LOC_Os03g02960 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301192756 NA 1.06E-06 mr1319 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
vg0301192756 NA 1.27E-08 mr1332 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
vg0301192756 NA 8.45E-07 mr1944 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
vg0301192756 2.70E-06 8.40E-07 mr1977 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
vg0301192756 7.07E-06 1.54E-06 mr1977 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