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Detailed information for vg0334059893:

Variant ID: vg0334059893 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34059893
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, G: 0.08, others allele: 0.00, population size: 35. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGAGATATAAATGAATGCGATGCTCTTGAATCGAAGAGAACTTTAGCTGGAGTGGAGTTGATAGAAAACGTACCCATCAGTACGCCCTGGTCTTCCTG[T/G]
GCCTCTTCAGCTCGAACGTGGTTCACTTGCCCGCGTCCAAATCCGGTAGCGGTCCTGTTAGTCTGCGGAGTCCTGAATAGACCTCGTCCAGCAGCAGGGG

Reverse complement sequence

CCCCTGCTGCTGGACGAGGTCTATTCAGGACTCCGCAGACTAACAGGACCGCTACCGGATTTGGACGCGGGCAAGTGAACCACGTTCGAGCTGAAGAGGC[A/C]
CAGGAAGACCAGGGCGTACTGATGGGTACGTTTTCTATCAACTCCACTCCAGCTAAAGTTCTCTTCGATTCAAGAGCATCGCATTCATTTATATCTCTGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.00% 7.10% 9.50% 1.44% NA
All Indica  2759 77.20% 9.90% 11.85% 0.98% NA
All Japonica  1512 99.70% 0.10% 0.07% 0.13% NA
Aus  269 43.90% 20.40% 35.69% 0.00% NA
Indica I  595 76.80% 2.50% 18.49% 2.18% NA
Indica II  465 65.20% 24.30% 10.11% 0.43% NA
Indica III  913 84.60% 7.10% 7.89% 0.44% NA
Indica Intermediate  786 76.20% 10.30% 12.47% 1.02% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.83% NA
VI/Aromatic  96 49.00% 1.00% 11.46% 38.54% NA
Intermediate  90 78.90% 3.30% 15.56% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0334059893 T -> DEL LOC_Os03g59810.1 N frameshift_variant Average:9.733; most accessible tissue: Zhenshan97 root, score: 16.934 N N N N
vg0334059893 T -> G LOC_Os03g59810.1 synonymous_variant ; p.Ala359Ala; LOW synonymous_codon Average:9.733; most accessible tissue: Zhenshan97 root, score: 16.934 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334059893 NA 2.50E-07 mr1291 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
vg0334059893 NA 2.48E-06 mr1399 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
vg0334059893 5.60E-06 NA mr1851 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
vg0334059893 1.57E-06 2.12E-08 mr1851 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
vg0334059893 NA 4.52E-06 mr1062_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
vg0334059893 NA 6.12E-10 mr1077_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
vg0334059893 NA 2.66E-08 mr1149_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
vg0334059893 NA 2.89E-07 mr1158_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
vg0334059893 NA 4.90E-08 mr1441_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
vg0334059893 NA 1.36E-09 mr1715_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
vg0334059893 NA 6.26E-06 mr1946_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
vg0334059893 NA 6.26E-06 mr1948_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