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Detailed information for vg1013156252:

Variant ID: vg1013156252 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 13156252
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.33, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGGTAAAATTGTCATTTCATTCATACTGCTGCATGCGAGGATGACTTAGCATGCTCACGTGGTATTTTTATGGGTCCAAGGACTATATTAACCCAAAT[G/A]
ATTAATTTGGGGGACTTGTTTGGATGATTTGAAACCTCAATGACCAAGCTGAGCCCGAAACGAAACTCAAGAACCATATGAGCTATTCACCCAAATTTAA

Reverse complement sequence

TTAAATTTGGGTGAATAGCTCATATGGTTCTTGAGTTTCGTTTCGGGCTCAGCTTGGTCATTGAGGTTTCAAATCATCCAAACAAGTCCCCCAAATTAAT[C/T]
ATTTGGGTTAATATAGTCCTTGGACCCATAAAAATACCACGTGAGCATGCTAAGTCATCCTCGCATGCAGCAGTATGAATGAAATGACAATTTTACCCTT

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 83.50% 16.40% 0.08% 0.00% NA
All Indica  2759 83.60% 16.30% 0.07% 0.00% NA
All Japonica  1512 79.80% 20.00% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 39.80% 59.80% 0.34% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 89.70% 10.30% 0.00% 0.00% NA
Temperate Japonica  767 97.40% 2.60% 0.00% 0.00% NA
Tropical Japonica  504 54.60% 45.00% 0.40% 0.00% NA
Japonica Intermediate  241 76.80% 23.20% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg1013156252 G -> A LOC_Os10g25430.1 upstream_gene_variant ; 2262.0bp to feature; MODIFIER silent_mutation Average:41.856; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg1013156252 G -> A LOC_Os10g25450.1 upstream_gene_variant ; 4039.0bp to feature; MODIFIER silent_mutation Average:41.856; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg1013156252 G -> A LOC_Os10g25430-LOC_Os10g25450 intergenic_region ; MODIFIER silent_mutation Average:41.856; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1013156252 NA 1.80E-12 mr1026 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
vg1013156252 NA 5.32E-10 mr1161 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
vg1013156252 1.09E-08 NA mr1533 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
vg1013156252 4.86E-08 5.35E-16 mr1533 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
vg1013156252 5.83E-09 NA mr1980 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
vg1013156252 NA 6.51E-15 mr1980 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
vg1013156252 NA 3.30E-09 mr1161_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
vg1013156252 3.78E-12 NA mr1533_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
vg1013156252 1.91E-09 7.03E-21 mr1533_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
vg1013156252 NA 1.16E-07 mr1578_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
vg1013156252 NA 2.81E-07 mr1745_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
vg1013156252 NA 2.84E-06 mr1843_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
vg1013156252 NA 3.52E-07 mr1904_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
vg1013156252 NA 2.75E-07 mr1952_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
vg1013156252 5.68E-06 NA mr1980_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
vg1013156252 NA 1.09E-09 mr1980_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