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Detailed information for vg0827102972:

Variant ID: vg0827102972 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 27102972
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTTGTCTCTAAACCCATCCACTTTCTTAGCTTGATAGTCACCCCCTTTTATTATTGCCAAAATCTTGTTTCGACAGTAATTACGTTATAACTACTACAC[A/G]
AGCTATCACTAAAATCTTACGCGCAACATGTGTAGATGGGAAAAAAAACTTGCGTAAGTTTTCTAGCAAATCTGTTTATTAGTTGAAAAGTTTGTTCTAA

Reverse complement sequence

TTAGAACAAACTTTTCAACTAATAAACAGATTTGCTAGAAAACTTACGCAAGTTTTTTTTCCCATCTACACATGTTGCGCGTAAGATTTTAGTGATAGCT[T/C]
GTGTAGTAGTTATAACGTAATTACTGTCGAAACAAGATTTTGGCAATAATAAAAGGGGGTGACTATCAAGCTAAGAAAGTGGATGGGTTTAGAGACAAGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.40% 6.80% 3.83% 0.00% NA
All Indica  2759 99.70% 0.10% 0.14% 0.00% NA
All Japonica  1512 68.00% 20.60% 11.38% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.10% 0.25% 0.00% NA
Temperate Japonica  767 46.90% 36.60% 16.43% 0.00% NA
Tropical Japonica  504 93.10% 2.40% 4.56% 0.00% NA
Japonica Intermediate  241 82.60% 7.90% 9.54% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 90.00% 5.60% 4.44% 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
vg0827102972 A -> G LOC_Os08g42860.1 upstream_gene_variant ; 1470.0bp to feature; MODIFIER silent_mutation Average:39.016; most accessible tissue: Callus, score: 75.169 N N N N
vg0827102972 A -> G LOC_Os08g42870.1 downstream_gene_variant ; 342.0bp to feature; MODIFIER silent_mutation Average:39.016; most accessible tissue: Callus, score: 75.169 N N N N
vg0827102972 A -> G LOC_Os08g42860-LOC_Os08g42870 intergenic_region ; MODIFIER silent_mutation Average:39.016; most accessible tissue: Callus, score: 75.169 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0827102972 NA 1.46E-09 mr1010_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
vg0827102972 NA 6.22E-06 mr1330_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
vg0827102972 NA 1.25E-06 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
vg0827102972 NA 7.08E-10 mr1576_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
vg0827102972 NA 2.58E-06 mr1576_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
vg0827102972 4.75E-07 NA mr1712_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
vg0827102972 NA 8.31E-07 mr1768_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
vg0827102972 2.08E-06 2.61E-09 mr1946_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
vg0827102972 2.08E-06 2.61E-09 mr1948_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
vg0827102972 6.58E-08 1.20E-10 mr1977_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
vg0827102972 NA 4.12E-07 mr1977_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