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Detailed information for vg1002138376:

Variant ID: vg1002138376 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2138376
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.63, A: 0.37, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


AAATCAGCTCTCCTCTTCCATTTTACACCCAATTTCAGGTCCCATGGCTGCCACATCATCAACCAAGGTGGCACTGAGAGCGTTAAAGGATGGGATTTGT[G/A]
CCTTACCCCAGCGGGCACTTAGATGGAGCCATAACCCCCAAAATCCAAACCCTAGACAATCCGATATGCAACAAAAACAACCAAATCTGAGACAAATTGT

Reverse complement sequence

ACAATTTGTCTCAGATTTGGTTGTTTTTGTTGCATATCGGATTGTCTAGGGTTTGGATTTTGGGGGTTATGGCTCCATCTAAGTGCCCGCTGGGGTAAGG[C/T]
ACAAATCCCATCCTTTAACGCTCTCAGTGCCACCTTGGTTGATGATGTGGCAGCCATGGGACCTGAAATTGGGTGTAAAATGGAAGAGGAGAGCTGATTT

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 35.30% 31.00% 1.80% 31.97% NA
All Indica  2759 15.40% 29.40% 2.17% 53.03% NA
All Japonica  1512 78.40% 20.40% 0.00% 1.26% NA
Aus  269 4.50% 84.80% 7.43% 3.35% NA
Indica I  595 4.40% 41.70% 4.87% 49.08% NA
Indica II  465 17.80% 18.90% 0.65% 62.58% NA
Indica III  913 20.70% 25.20% 1.75% 52.35% NA
Indica Intermediate  786 16.20% 31.20% 1.53% 51.15% NA
Temperate Japonica  767 79.40% 19.90% 0.00% 0.65% NA
Tropical Japonica  504 80.20% 17.50% 0.00% 2.38% NA
Japonica Intermediate  241 71.40% 27.80% 0.00% 0.83% NA
VI/Aromatic  96 11.50% 81.20% 3.12% 4.17% NA
Intermediate  90 37.80% 42.20% 2.22% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1002138376 G -> A LOC_Os10g04500.1 upstream_gene_variant ; 4872.0bp to feature; MODIFIER silent_mutation Average:26.177; most accessible tissue: Zhenshan97 flag leaf, score: 54.545 N N N N
vg1002138376 G -> A LOC_Os10g04510.1 upstream_gene_variant ; 4988.0bp to feature; MODIFIER silent_mutation Average:26.177; most accessible tissue: Zhenshan97 flag leaf, score: 54.545 N N N N
vg1002138376 G -> A LOC_Os10g04500-LOC_Os10g04510 intergenic_region ; MODIFIER silent_mutation Average:26.177; most accessible tissue: Zhenshan97 flag leaf, score: 54.545 N N N N
vg1002138376 G -> DEL N N silent_mutation Average:26.177; most accessible tissue: Zhenshan97 flag leaf, score: 54.545 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002138376 3.55E-06 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
vg1002138376 NA 6.52E-08 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
vg1002138376 NA 6.41E-06 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
vg1002138376 1.19E-07 NA mr1486_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
vg1002138376 NA 2.80E-08 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