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Detailed information for vg0204782959:

Variant ID: vg0204782959 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4782959
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.27, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


AACCTGTTGTTGGTCTGGGACCCCTCTCGTCGGCATATGGCAATCCTGTGTCTGCTCTCGAAATGCCTTGTCATGAAAGCCCTTAGGTCACCAGACGTGG[T/C]
CGTTCTACACGGGCTAGGTGATTCGGGTTAGTAATGTCGTGTGGGTAAAGTGTACCCCCTCTGCAGAGGTTAACAAACTGTTCGAACAGCCGTGCCCACG

Reverse complement sequence

CGTGGGCACGGCTGTTCGAACAGTTTGTTAACCTCTGCAGAGGGGGTACACTTTACCCACACGACATTACTAACCCGAATCACCTAGCCCGTGTAGAACG[A/G]
CCACGTCTGGTGACCTAAGGGCTTTCATGACAAGGCATTTCGAGAGCAGACACAGGATTGCCATATGCCGACGAGAGGGGTCCCAGACCAACAACAGGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.90% 21.10% 12.38% 3.60% NA
All Indica  2759 89.80% 1.70% 7.79% 0.69% NA
All Japonica  1512 10.70% 60.20% 19.58% 9.52% NA
Aus  269 79.20% 4.80% 14.87% 1.12% NA
Indica I  595 94.30% 1.20% 3.19% 1.34% NA
Indica II  465 87.70% 2.40% 9.25% 0.65% NA
Indica III  913 88.50% 1.40% 9.75% 0.33% NA
Indica Intermediate  786 89.10% 2.20% 8.14% 0.64% NA
Temperate Japonica  767 0.90% 93.90% 2.35% 2.87% NA
Tropical Japonica  504 18.50% 17.70% 46.23% 17.66% NA
Japonica Intermediate  241 25.70% 41.90% 18.67% 13.69% NA
VI/Aromatic  96 80.20% 2.10% 17.71% 0.00% NA
Intermediate  90 51.10% 25.60% 18.89% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0204782959 T -> DEL N N silent_mutation Average:15.953; most accessible tissue: Callus, score: 26.201 N N N N
vg0204782959 T -> C LOC_Os02g09280.1 upstream_gene_variant ; 2688.0bp to feature; MODIFIER silent_mutation Average:15.953; most accessible tissue: Callus, score: 26.201 N N N N
vg0204782959 T -> C LOC_Os02g09290.1 upstream_gene_variant ; 2244.0bp to feature; MODIFIER silent_mutation Average:15.953; most accessible tissue: Callus, score: 26.201 N N N N
vg0204782959 T -> C LOC_Os02g09300.1 downstream_gene_variant ; 4888.0bp to feature; MODIFIER silent_mutation Average:15.953; most accessible tissue: Callus, score: 26.201 N N N N
vg0204782959 T -> C LOC_Os02g09280-LOC_Os02g09290 intergenic_region ; MODIFIER silent_mutation Average:15.953; most accessible tissue: Callus, score: 26.201 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204782959 NA 4.98E-08 mr1031_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
vg0204782959 NA 4.21E-06 mr1077_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
vg0204782959 NA 3.39E-12 mr1087_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
vg0204782959 NA 1.46E-08 mr1090_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
vg0204782959 NA 1.60E-08 mr1091_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
vg0204782959 NA 5.36E-06 mr1094_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
vg0204782959 NA 4.71E-08 mr1096_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
vg0204782959 NA 7.61E-06 mr1112_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
vg0204782959 NA 1.09E-06 mr1211_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
vg0204782959 7.03E-06 7.03E-06 mr1234_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
vg0204782959 NA 4.35E-09 mr1235_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
vg0204782959 NA 4.49E-13 mr1241_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
vg0204782959 NA 3.19E-06 mr1246_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
vg0204782959 NA 3.85E-07 mr1350_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
vg0204782959 NA 3.85E-06 mr1404_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
vg0204782959 NA 1.01E-10 mr1526_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
vg0204782959 NA 9.84E-09 mr1798_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
vg0204782959 NA 1.49E-08 mr1808_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
vg0204782959 NA 5.63E-06 mr1861_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
vg0204782959 NA 3.57E-09 mr1862_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