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Detailed information for vg1001424035:

Variant ID: vg1001424035 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1424035
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GTCTGGATTTTTGTTCTGCCTGAATGGAGGCGCTGTGAGTTGGAAGATTTCCAAGCAAGATACAGTCGCTGATCCTACAACAGAAGCCGAATACATTGCC[G/A]
CTTCTGAAGCAGCAAAGGAGGCTGTTTGGACCTCTATTGCGATATTAGTGGTGCCATTGCGCAAGCCAAGGAGCCTAGATCGCATCAAAAGTCCGAACAC

Reverse complement sequence

GTGTTCGGACTTTTGATGCGATCTAGGCTCCTTGGCTTGCGCAATGGCACCACTAATATCGCAATAGAGGTCCAAACAGCCTCCTTTGCTGCTTCAGAAG[C/T]
GGCAATGTATTCGGCTTCTGTTGTAGGATCAGCGACTGTATCTTGCTTGGAAATCTTCCAACTCACAGCGCCTCCATTCAGGCAGAACAAAAATCCAGAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 30.30% 0.72% 2.31% NA
All Indica  2759 45.00% 50.50% 0.98% 3.52% NA
All Japonica  1512 98.30% 1.50% 0.00% 0.13% NA
Aus  269 97.40% 0.00% 0.74% 1.86% NA
Indica I  595 43.20% 54.30% 1.18% 1.34% NA
Indica II  465 38.30% 59.40% 0.22% 2.15% NA
Indica III  913 48.40% 44.00% 1.10% 6.46% NA
Indica Intermediate  786 46.40% 49.90% 1.15% 2.54% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 1.70% 0.00% 0.83% NA
VI/Aromatic  96 91.70% 0.00% 4.17% 4.17% NA
Intermediate  90 80.00% 17.80% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001424035 G -> A LOC_Os10g03350.1 downstream_gene_variant ; 262.0bp to feature; MODIFIER silent_mutation Average:29.578; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 N N N N
vg1001424035 G -> A LOC_Os10g03350-LOC_Os10g03360 intergenic_region ; MODIFIER silent_mutation Average:29.578; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 N N N N
vg1001424035 G -> DEL N N silent_mutation Average:29.578; most accessible tissue: Zhenshan97 flag leaf, score: 49.013 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001424035 1.05E-10 NA mr1486 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
vg1001424035 2.62E-12 1.70E-13 mr1486 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
vg1001424035 3.89E-09 NA mr1548 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
vg1001424035 2.86E-09 9.32E-10 mr1548 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
vg1001424035 7.51E-06 4.90E-06 mr1588 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
vg1001424035 NA 1.66E-06 mr1721 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
vg1001424035 1.58E-09 NA mr1486_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
vg1001424035 1.81E-11 3.34E-12 mr1486_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
vg1001424035 1.55E-06 NA mr1588_2 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
vg1001424035 8.23E-10 NA mr1721_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
vg1001424035 9.72E-09 3.52E-11 mr1721_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