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Detailed information for vg0804502899:

Variant ID: vg0804502899 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4502899
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, T: 0.35, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CTCGGACCCGGTGGTTTAGGAACCCTGCTAAGCACTGGTCCGGTTTTTCTTACACCACGGGTTCGGTTCGATTTTTACAACTAGACTATTGAGATGCCAC[T/C]
GGAGAGAATAATTCTTTGCAAATGCCAATTTTGCATATGTAGAAGGACATGTCACATTACCAACATGGAGGTGGCAAGAAAATGACCCATTTGCCCTTGT

Reverse complement sequence

ACAAGGGCAAATGGGTCATTTTCTTGCCACCTCCATGTTGGTAATGTGACATGTCCTTCTACATATGCAAAATTGGCATTTGCAAAGAATTATTCTCTCC[A/G]
GTGGCATCTCAATAGTCTAGTTGTAAAAATCGAACCGAACCCGTGGTGTAAGAAAAACCGGACCAGTGCTTAGCAGGGTTCCTAAACCACCGGGTCCGAG

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 86.80% 13.10% 0.08% 0.00% NA
All Indica  2759 97.50% 2.50% 0.04% 0.00% NA
All Japonica  1512 64.40% 35.40% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.80% 5.20% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 1.90% 0.13% 0.00% NA
Temperate Japonica  767 75.50% 24.10% 0.39% 0.00% NA
Tropical Japonica  504 37.30% 62.70% 0.00% 0.00% NA
Japonica Intermediate  241 85.50% 14.50% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0804502899 T -> C LOC_Os08g07960.1 upstream_gene_variant ; 657.0bp to feature; MODIFIER silent_mutation Average:58.382; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0804502899 T -> C LOC_Os08g07960.2 upstream_gene_variant ; 657.0bp to feature; MODIFIER silent_mutation Average:58.382; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0804502899 T -> C LOC_Os08g07970.1 downstream_gene_variant ; 2839.0bp to feature; MODIFIER silent_mutation Average:58.382; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0804502899 T -> C LOC_Os08g07970.3 downstream_gene_variant ; 2839.0bp to feature; MODIFIER silent_mutation Average:58.382; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0804502899 T -> C LOC_Os08g07970.2 downstream_gene_variant ; 2846.0bp to feature; MODIFIER silent_mutation Average:58.382; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0804502899 T -> C LOC_Os08g07960-LOC_Os08g07970 intergenic_region ; MODIFIER silent_mutation Average:58.382; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804502899 NA 1.83E-06 mr1002 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
vg0804502899 4.27E-07 NA mr1519 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