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Detailed information for vg0514648404:

Variant ID: vg0514648404 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 14648404
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


TGCAATTTGAATTAATTTATGCGGAGAAAGAAAATGAGAGAAGTGCATGACATGTGGACTAGCCATCATTTTTTCCCCCTTATTGATTGGATTAACATAA[C/T]
ATAAGATAAGACCATAATGGTGTAAGTTTACCGATGCAAAATGTTTGTTTGGTTGAGAGGTAAAAAGCATCCAGCTTGGAATTTGTGATTGGATTTTAAC

Reverse complement sequence

GTTAAAATCCAATCACAAATTCCAAGCTGGATGCTTTTTACCTCTCAACCAAACAAACATTTTGCATCGGTAAACTTACACCATTATGGTCTTATCTTAT[G/A]
TTATGTTAATCCAATCAATAAGGGGGAAAAAATGATGGCTAGTCCACATGTCATGCACTTCTCTCATTTTCTTTCTCCGCATAAATTAATTCAAATTGCA

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 51.40% 48.30% 0.28% 0.00% NA
All Indica  2759 22.80% 76.80% 0.47% 0.00% NA
All Japonica  1512 98.00% 2.00% 0.00% 0.00% NA
Aus  269 62.10% 37.90% 0.00% 0.00% NA
Indica I  595 23.40% 75.80% 0.84% 0.00% NA
Indica II  465 25.20% 74.40% 0.43% 0.00% NA
Indica III  913 23.20% 76.70% 0.11% 0.00% NA
Indica Intermediate  786 20.40% 79.00% 0.64% 0.00% NA
Temperate Japonica  767 97.10% 2.90% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 64.40% 35.60% 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
vg0514648404 C -> T LOC_Os05g25240.1 downstream_gene_variant ; 406.0bp to feature; MODIFIER silent_mutation Average:40.371; most accessible tissue: Callus, score: 73.401 N N N N
vg0514648404 C -> T LOC_Os05g25240-LOC_Os05g25250 intergenic_region ; MODIFIER silent_mutation Average:40.371; most accessible tissue: Callus, score: 73.401 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0514648404 1.26E-06 1.78E-29 mr1039 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
vg0514648404 NA 2.96E-27 mr1632 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
vg0514648404 NA 3.00E-06 mr1632 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
vg0514648404 3.73E-10 7.57E-37 mr1039_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
vg0514648404 1.01E-08 1.73E-09 mr1039_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
vg0514648404 NA 6.27E-07 mr1275_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
vg0514648404 NA 4.91E-06 mr1320_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
vg0514648404 NA 5.78E-13 mr1514_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
vg0514648404 1.24E-11 9.15E-41 mr1632_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
vg0514648404 1.79E-09 5.98E-11 mr1632_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
vg0514648404 1.05E-07 6.47E-33 mr1873_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
vg0514648404 1.97E-09 5.52E-09 mr1873_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