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Detailed information for vg0217569334:

Variant ID: vg0217569334 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17569334
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


TGCTTATATATAGATGGTATATATTAGCTTTTTAAATTTGAATGATAATATATTTAGGATTTTACGAACTCGGACAATGTTGACGCAATGACTCCGAGCT[T/C]
TTGCTTATAGAAAAGAACATGTCATGCGTGGATAAAAGAACGGTTAACATAAATCATAAGCATGGCAATGGAGAGTCCTCGACGAAGAAAAGGTAAACGA

Reverse complement sequence

TCGTTTACCTTTTCTTCGTCGAGGACTCTCCATTGCCATGCTTATGATTTATGTTAACCGTTCTTTTATCCACGCATGACATGTTCTTTTCTATAAGCAA[A/G]
AGCTCGGAGTCATTGCGTCAACATTGTCCGAGTTCGTAAAATCCTAAATATATTATCATTCAAATTTAAAAAGCTAATATATACCATCTATATATAAGCA

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 53.80% 46.00% 0.19% 0.00% NA
All Indica  2759 76.50% 23.10% 0.33% 0.00% NA
All Japonica  1512 1.70% 98.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.70% 1.00% 0.34% 0.00% NA
Indica II  465 83.20% 16.80% 0.00% 0.00% NA
Indica III  913 54.00% 45.70% 0.33% 0.00% NA
Indica Intermediate  786 82.10% 17.40% 0.51% 0.00% NA
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 1.60% 98.40% 0.00% 0.00% NA
Japonica Intermediate  241 2.90% 97.10% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 57.80% 42.20% 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
vg0217569334 T -> C LOC_Os02g29540.1 upstream_gene_variant ; 4594.0bp to feature; MODIFIER silent_mutation Average:52.13; most accessible tissue: Zhenshan97 root, score: 81.974 N N N N
vg0217569334 T -> C LOC_Os02g29540-LOC_Os02g29550 intergenic_region ; MODIFIER silent_mutation Average:52.13; most accessible tissue: Zhenshan97 root, score: 81.974 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217569334 NA 2.74E-13 mr1138 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
vg0217569334 NA 5.15E-06 mr1138 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
vg0217569334 NA 1.36E-07 mr1354 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
vg0217569334 NA 6.19E-09 mr1806 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
vg0217569334 2.95E-06 NA mr1036_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
vg0217569334 2.12E-06 1.55E-16 mr1138_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
vg0217569334 NA 1.19E-08 mr1138_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
vg0217569334 7.29E-06 NA mr1169_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
vg0217569334 NA 6.65E-09 mr1354_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
vg0217569334 NA 5.54E-06 mr1354_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
vg0217569334 NA 3.60E-12 mr1806_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