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Detailed information for vg0809709071:

Variant ID: vg0809709071 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9709071
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


AAGATACAGTAGCGAAGAGATAAGCAGGAGGCACAGGCGACGCCACCCCTGGCCTCTATAAAAGGAGACGTTGGCCTTCACTCCGGGGAGACAGAACCAC[G/A]
AAGACACCATTCAGAGAAAAGCTTCCAAGCGCGCTCTCACCCTCCATTCCATCTTTCTTAGTAGTAGTTCCTCTAGCCTACCTTGCATAATATATATTGA

Reverse complement sequence

TCAATATATATTATGCAAGGTAGGCTAGAGGAACTACTACTAAGAAAGATGGAATGGAGGGTGAGAGCGCGCTTGGAAGCTTTTCTCTGAATGGTGTCTT[C/T]
GTGGTTCTGTCTCCCCGGAGTGAAGGCCAACGTCTCCTTTTATAGAGGCCAGGGGTGGCGTCGCCTGTGCCTCCTGCTTATCTCTTCGCTACTGTATCTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 42.40% 41.20% 11.47% 4.87% NA
All Indica  2759 65.70% 22.60% 11.27% 0.40% NA
All Japonica  1512 2.40% 82.90% 0.99% 13.76% NA
Aus  269 42.80% 3.70% 53.16% 0.37% NA
Indica I  595 82.90% 16.80% 0.34% 0.00% NA
Indica II  465 47.10% 17.40% 34.19% 1.29% NA
Indica III  913 64.30% 27.70% 7.89% 0.11% NA
Indica Intermediate  786 65.40% 24.20% 9.92% 0.51% NA
Temperate Japonica  767 2.00% 94.30% 1.30% 2.48% NA
Tropical Japonica  504 2.40% 65.70% 0.20% 31.75% NA
Japonica Intermediate  241 3.70% 82.60% 1.66% 12.03% NA
VI/Aromatic  96 12.50% 12.50% 66.67% 8.33% NA
Intermediate  90 33.30% 54.40% 10.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0809709071 G -> A LOC_Os08g15940.1 upstream_gene_variant ; 2852.0bp to feature; MODIFIER silent_mutation Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 N N N N
vg0809709071 G -> A LOC_Os08g15960.1 upstream_gene_variant ; 1882.0bp to feature; MODIFIER silent_mutation Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 N N N N
vg0809709071 G -> A LOC_Os08g15930.1 downstream_gene_variant ; 4932.0bp to feature; MODIFIER silent_mutation Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 N N N N
vg0809709071 G -> A LOC_Os08g15950.1 downstream_gene_variant ; 787.0bp to feature; MODIFIER silent_mutation Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 N N N N
vg0809709071 G -> A LOC_Os08g15950-LOC_Os08g15960 intergenic_region ; MODIFIER silent_mutation Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 N N N N
vg0809709071 G -> DEL N N silent_mutation Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809709071 NA 1.16E-10 mr1595_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
vg0809709071 NA 8.65E-12 mr1600_2 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