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Detailed information for vg1208480660:

Variant ID: vg1208480660 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8480660
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCTCCACCAGTGCTTCCGCTGGAATGATTTCTCTGTTAAAATTTGTCGGTCCCTACAACATCGTTCAGAAGAAGAATGATGTAGCACATCGAGTTAGG[A/G]
CATCATTTTAATCCATGCGGGTTGGTGGTGAGTGTAACAACCAGCCAGTTCAAAGCCTACCGTCATGGTGTACGTATTATGCGGTTTAGACCCATCCGCC

Reverse complement sequence

GGCGGATGGGTCTAAACCGCATAATACGTACACCATGACGGTAGGCTTTGAACTGGCTGGTTGTTACACTCACCACCAACCCGCATGGATTAAAATGATG[T/C]
CCTAACTCGATGTGCTACATCATTCTTCTTCTGAACGATGTTGTAGGGACCGACAAATTTTAACAGAGAAATCATTCCAGCGGAAGCACTGGTGGAGAAA

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 70.70% 29.20% 0.15% 0.00% NA
All Indica  2759 62.90% 36.90% 0.22% 0.00% NA
All Japonica  1512 96.70% 3.30% 0.00% 0.00% NA
Aus  269 14.90% 84.80% 0.37% 0.00% NA
Indica I  595 62.20% 37.30% 0.50% 0.00% NA
Indica II  465 54.00% 45.80% 0.22% 0.00% NA
Indica III  913 69.30% 30.60% 0.11% 0.00% NA
Indica Intermediate  786 61.30% 38.50% 0.13% 0.00% NA
Temperate Japonica  767 94.80% 5.20% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg1208480660 A -> G LOC_Os12g14820.1 downstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:45.388; most accessible tissue: Minghui63 root, score: 81.325 N N N N
vg1208480660 A -> G LOC_Os12g14820-LOC_Os12g14830 intergenic_region ; MODIFIER silent_mutation Average:45.388; most accessible tissue: Minghui63 root, score: 81.325 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208480660 3.20E-08 NA mr1425 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
vg1208480660 7.89E-08 9.21E-12 mr1425 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
vg1208480660 NA 3.16E-06 mr1558 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
vg1208480660 NA 6.28E-06 mr1002_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
vg1208480660 NA 1.72E-07 mr1683_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
vg1208480660 NA 5.69E-08 mr1864_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