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Detailed information for vg0200846970:

Variant ID: vg0200846970 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 846970
Reference Allele: GAlternative Allele: T,A
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


GTAGGGAAAAAGAAGGAACCATTGTGTTTTGGAAACACTTTGGGCGTTGGGTAAATGGTGTATATGAAAAATGTACACAACATGATGAGGAGAGTATTTT[G/T,A]
TAAAATGTATCGTGGGGATGGCGGGGCTGACAAGTCTTCATACAGGCTGCACATTTTGGATCCAATGATCCACGATCGAATTTACAATTTTCCATGTAGG

Reverse complement sequence

CCTACATGGAAAATTGTAAATTCGATCGTGGATCATTGGATCCAAAATGTGCAGCCTGTATGAAGACTTGTCAGCCCCGCCATCCCCACGATACATTTTA[C/A,T]
AAAATACTCTCCTCATCATGTTGTGTACATTTTTCATATACACCATTTACCCAACGCCCAAAGTGTTTCCAAAACACAATGGTTCCTTCTTTTTCCCTAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.10% 6.50% 0.42% 0.00% A: 0.04%
All Indica  2759 95.30% 4.50% 0.14% 0.00% NA
All Japonica  1512 87.50% 11.50% 0.99% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 79.60% 19.80% 0.65% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 4.10% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.00% 0.39% 0.00% NA
Tropical Japonica  504 64.10% 33.70% 2.18% 0.00% NA
Japonica Intermediate  241 97.90% 1.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 6.70% 1.11% 0.00% A: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0200846970 G -> A LOC_Os02g02410.1 upstream_gene_variant ; 4298.0bp to feature; MODIFIER silent_mutation Average:29.305; most accessible tissue: Callus, score: 56.616 N N N N
vg0200846970 G -> A LOC_Os02g02410-LOC_Os02g02424 intergenic_region ; MODIFIER silent_mutation Average:29.305; most accessible tissue: Callus, score: 56.616 N N N N
vg0200846970 G -> T LOC_Os02g02410.1 upstream_gene_variant ; 4298.0bp to feature; MODIFIER silent_mutation Average:29.305; most accessible tissue: Callus, score: 56.616 N N N N
vg0200846970 G -> T LOC_Os02g02410-LOC_Os02g02424 intergenic_region ; MODIFIER silent_mutation Average:29.305; most accessible tissue: Callus, score: 56.616 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200846970 NA 1.04E-07 mr1076 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
vg0200846970 NA 1.45E-07 mr1082 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
vg0200846970 NA 6.34E-09 mr1083 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
vg0200846970 NA 7.54E-08 mr1226 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
vg0200846970 NA 1.96E-06 mr1742 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
vg0200846970 1.28E-09 1.28E-09 mr1076_2 Jap_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
vg0200846970 4.61E-06 1.30E-10 mr1082_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
vg0200846970 4.68E-08 1.45E-11 mr1083_2 Jap_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
vg0200846970 1.60E-06 7.64E-06 mr1085_2 Jap_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
vg0200846970 1.80E-06 2.53E-07 mr1103_2 Jap_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
vg0200846970 1.97E-06 2.34E-07 mr1104_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
vg0200846970 NA 1.91E-06 mr1107_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
vg0200846970 2.63E-06 2.63E-06 mr1145_2 Jap_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
vg0200846970 4.06E-06 NA mr1155_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
vg0200846970 6.63E-06 NA mr1226_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
vg0200846970 1.20E-07 2.17E-10 mr1226_2 Jap_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
vg0200846970 7.92E-08 2.54E-09 mr1408_2 Jap_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
vg0200846970 8.52E-06 NA mr1437_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