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Detailed information for vg0434528001:

Variant ID: vg0434528001 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34528001
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, T: 0.10, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


TATATCACTTTTCAATAAATATTTTTATAGAAACAAGAAGTCAAAGTTATGTTTTGGAGACCGTGTCGCTGTTCTAAACGACTTCCTTTACGAGTACAGA[T/G]
GGAGTACTCGACAGTTAAACTTGCTTGAAAAGCTGTTACAGCTTCACCTTGTCTATGCCATGTCTGCTTGCTTAAACTTGACTATGGTTCTGTTCACTTT

Reverse complement sequence

AAAGTGAACAGAACCATAGTCAAGTTTAAGCAAGCAGACATGGCATAGACAAGGTGAAGCTGTAACAGCTTTTCAAGCAAGTTTAACTGTCGAGTACTCC[A/C]
TCTGTACTCGTAAAGGAAGTCGTTTAGAACAGCGACACGGTCTCCAAAACATAACTTTGACTTCTTGTTTCTATAAAAATATTTATTGAAAAGTGATATA

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 61.00% 38.30% 0.34% 0.30% NA
All Indica  2759 96.40% 2.80% 0.36% 0.47% NA
All Japonica  1512 11.60% 88.00% 0.26% 0.07% NA
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 97.60% 1.20% 0.67% 0.50% NA
Indica II  465 97.40% 1.10% 0.43% 1.08% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 91.90% 7.00% 0.51% 0.64% NA
Temperate Japonica  767 4.40% 95.30% 0.13% 0.13% NA
Tropical Japonica  504 6.90% 92.70% 0.40% 0.00% NA
Japonica Intermediate  241 44.40% 55.20% 0.41% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 46.70% 51.10% 2.22% 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
vg0434528001 T -> DEL N N silent_mutation Average:33.096; most accessible tissue: Callus, score: 72.525 N N N N
vg0434528001 T -> G LOC_Os04g57950.1 downstream_gene_variant ; 4422.0bp to feature; MODIFIER silent_mutation Average:33.096; most accessible tissue: Callus, score: 72.525 N N N N
vg0434528001 T -> G LOC_Os04g57950-LOC_Os04g57970 intergenic_region ; MODIFIER silent_mutation Average:33.096; most accessible tissue: Callus, score: 72.525 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434528001 NA 2.92E-13 mr1013 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
vg0434528001 NA 1.36E-09 mr1151 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
vg0434528001 NA 3.74E-08 mr1693 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
vg0434528001 NA 2.64E-12 mr1151_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
vg0434528001 1.06E-06 NA mr1187_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
vg0434528001 NA 7.77E-10 mr1349_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
vg0434528001 NA 5.10E-33 mr1571_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
vg0434528001 NA 4.62E-06 mr1720_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
vg0434528001 NA 1.05E-11 mr1728_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
vg0434528001 NA 2.96E-29 mr1825_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
vg0434528001 NA 1.54E-08 mr1860_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
vg0434528001 NA 1.04E-22 mr1924_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
vg0434528001 NA 2.78E-28 mr1943_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