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Detailed information for vg0141382072:

Variant ID: vg0141382072 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41382072
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, A: 0.13, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGAGAGGATAGGGGAGAGAGACGAAGAGAGGATAGAGGAGGAAGAAGAATGGCCGGGAGAGGGAGGAGAGAGAAGAGGAGGGAGTGAGAATGACACGT[A/G]
GGACCCACGTCGGCCACACTATTTTTAATTATTATTTTTATTGTCGTGGGATAAAGACTGAGTCAAACTAGTCACGTAGGCGCCACGTCAGCTAAAAACA

Reverse complement sequence

TGTTTTTAGCTGACGTGGCGCCTACGTGACTAGTTTGACTCAGTCTTTATCCCACGACAATAAAAATAATAATTAAAAATAGTGTGGCCGACGTGGGTCC[T/C]
ACGTGTCATTCTCACTCCCTCCTCTTCTCTCTCCTCCCTCTCCCGGCCATTCTTCTTCCTCCTCTATCCTCTCTTCGTCTCTCTCCCCTATCCTCTCTTT

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 84.40% 15.50% 0.08% 0.00% NA
All Indica  2759 81.40% 18.60% 0.07% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 63.90% 35.70% 0.37% 0.00% NA
Indica I  595 73.10% 26.70% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 74.90% 25.10% 0.00% 0.00% NA
Indica Intermediate  786 84.10% 15.80% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 1.11% 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
vg0141382072 A -> G LOC_Os01g71420.1 downstream_gene_variant ; 2214.0bp to feature; MODIFIER silent_mutation Average:61.605; most accessible tissue: Callus, score: 91.874 N N N N
vg0141382072 A -> G LOC_Os01g71410-LOC_Os01g71420 intergenic_region ; MODIFIER silent_mutation Average:61.605; most accessible tissue: Callus, score: 91.874 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141382072 NA 1.03E-08 mr1706 Ind_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
vg0141382072 NA 2.82E-07 mr1180_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
vg0141382072 NA 4.49E-06 mr1545_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
vg0141382072 NA 3.45E-06 mr1743_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
vg0141382072 NA 5.11E-06 mr1994_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