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Detailed information for vg0432879824:

Variant ID: vg0432879824 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32879824
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 34. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGGTAGTACGAATCGCTACGCTTCGCTTCTTTTTCACCGTCGGTTGCTGCGCTCCCTGCGGGTAATAGCAAGAGAGTGAAGAACGAACGATCATCAGT[T/C]
AGCAGTGAATGAGTCCGACTTGAGTTCGTGAGTCAAAGGCGTGGCAAGAGAGCGAGTTCGACTCGCGAACGACCTGCAAGTGAAGGACCGATCCTTTAAC

Reverse complement sequence

GTTAAAGGATCGGTCCTTCACTTGCAGGTCGTTCGCGAGTCGAACTCGCTCTCTTGCCACGCCTTTGACTCACGAACTCAAGTCGGACTCATTCACTGCT[A/G]
ACTGATGATCGTTCGTTCTTCACTCTCTTGCTATTACCCGCAGGGAGCGCAGCAACCGACGGTGAAAAAGAAGCGAAGCGTAGCGATTCGTACTACCGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 28.10% 0.10% 9.06% 62.70% NA
All Indica  2759 3.20% 0.20% 3.41% 93.26% NA
All Japonica  1512 70.50% 0.00% 19.97% 9.52% NA
Aus  269 44.20% 0.40% 1.12% 54.28% NA
Indica I  595 4.00% 0.20% 2.86% 92.94% NA
Indica II  465 2.40% 0.20% 3.23% 94.19% NA
Indica III  913 1.40% 0.10% 5.59% 92.88% NA
Indica Intermediate  786 5.00% 0.30% 1.40% 93.38% NA
Temperate Japonica  767 90.50% 0.00% 8.74% 0.78% NA
Tropical Japonica  504 44.20% 0.00% 30.36% 25.40% NA
Japonica Intermediate  241 61.80% 0.00% 34.02% 4.15% NA
VI/Aromatic  96 24.00% 0.00% 20.83% 55.21% NA
Intermediate  90 37.80% 0.00% 10.00% 52.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0432879824 T -> C LOC_Os04g55300-LOC_Os04g55310 intergenic_region ; MODIFIER silent_mutation Average:10.951; most accessible tissue: Callus, score: 35.095 N N N N
vg0432879824 T -> DEL N N silent_mutation Average:10.951; most accessible tissue: Callus, score: 35.095 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432879824 NA 5.14E-06 mr1448 Jap_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
vg0432879824 5.49E-06 8.89E-09 mr1072_2 Jap_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
vg0432879824 NA 3.68E-07 mr1075_2 Jap_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
vg0432879824 NA 2.90E-08 mr1077_2 Jap_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
vg0432879824 NA 9.24E-06 mr1149_2 Jap_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
vg0432879824 NA 1.91E-07 mr1441_2 Jap_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
vg0432879824 NA 6.56E-07 mr1568_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