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Detailed information for vg0803272035:

Variant ID: vg0803272035 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 3272035
Reference Allele: TAlternative Allele: C
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: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTAGAACGATTCTCCGACGACAAGGCTGGGGGCTAGGGAGAGTGTATAACTCAACAAACTGACTGATCGAAGTCGGTAAAAGAGTATACGCTCATATA[T/C]
AAAACATTGGTCTGTAAATTTGATTTTCAATTTTCCATACATATTATAACATGTCACCCTTTGAGCGTTCACTCGGGGGCTATTTCTATCTAATATTCTT

Reverse complement sequence

AAGAATATTAGATAGAAATAGCCCCCGAGTGAACGCTCAAAGGGTGACATGTTATAATATGTATGGAAAATTGAAAATCAAATTTACAGACCAATGTTTT[A/G]
TATATGAGCGTATACTCTTTTACCGACTTCGATCAGTCAGTTTGTTGAGTTATACACTCTCCCTAGCCCCCAGCCTTGTCGTCGGAGAATCGTTCTAGGA

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 63.10% 36.90% 0.08% 0.00% NA
All Indica  2759 84.80% 15.20% 0.07% 0.00% NA
All Japonica  1512 15.60% 84.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 90.90% 8.90% 0.17% 0.00% NA
Indica II  465 45.80% 54.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 85.80% 14.10% 0.13% 0.00% NA
Temperate Japonica  767 20.90% 79.10% 0.00% 0.00% NA
Tropical Japonica  504 11.30% 88.70% 0.00% 0.00% NA
Japonica Intermediate  241 7.90% 92.10% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 53.30% 44.40% 2.22% 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
vg0803272035 T -> C LOC_Os08g06000.1 upstream_gene_variant ; 640.0bp to feature; MODIFIER silent_mutation Average:45.729; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 N N N N
vg0803272035 T -> C LOC_Os08g06000-LOC_Os08g06010 intergenic_region ; MODIFIER silent_mutation Average:45.729; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0803272035 NA 1.11E-06 mr1062 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
vg0803272035 NA 2.51E-06 mr1167 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
vg0803272035 NA 3.06E-06 mr1535 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
vg0803272035 1.99E-06 1.99E-06 mr1726 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
vg0803272035 NA 9.94E-06 mr1536_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
vg0803272035 NA 8.61E-08 mr1765_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