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Detailed information for vg0528941797:

Variant ID: vg0528941797 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 28941797
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


CATGTTGGTAGTTCCTCTAACTTATTTTCATGTCTGTTCAGATCCTTTTCATGAAGTGAGAAGAAAGCGTGACAAGAAAAAGGAGGTAAGCATATGAACT[C/A]
TGAATTCTATATGCTGCCAGTTCTTAAGGAAATTCACTGTTTGGTTTTCCTCCCTGTTTATTTTGTGTGAGTTTTCCATCTCAATGCGAATATAGTGTCA

Reverse complement sequence

TGACACTATATTCGCATTGAGATGGAAAACTCACACAAAATAAACAGGGAGGAAAACCAAACAGTGAATTTCCTTAAGAACTGGCAGCATATAGAATTCA[G/T]
AGTTCATATGCTTACCTCCTTTTTCTTGTCACGCTTTCTTCTCACTTCATGAAAAGGATCTGAACAGACATGAAAATAAGTTAGAGGAACTACCAACATG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.90% 14.10% 0.00% 0.00% NA
All Indica  2759 77.20% 22.80% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 37.60% 62.40% 0.00% 0.00% NA
Indica II  465 77.40% 22.60% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 81.00% 19.00% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 82.20% 17.80% 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
vg0528941797 C -> A LOC_Os05g50480.1 intron_variant ; MODIFIER silent_mutation Average:55.37; most accessible tissue: Callus, score: 81.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0528941797 2.16E-06 NA mr1065 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
vg0528941797 NA 7.82E-10 mr1065 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
vg0528941797 NA 7.77E-11 mr1067 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
vg0528941797 8.09E-06 NA mr1110 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
vg0528941797 NA 3.02E-07 mr1221 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
vg0528941797 NA 2.04E-08 mr1234 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
vg0528941797 NA 5.24E-07 mr1850 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
vg0528941797 NA 1.39E-10 mr1067_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
vg0528941797 NA 1.06E-10 mr1234_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