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Detailed information for vg0212130167:

Variant ID: vg0212130167 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 12130167
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTTTTTTTTTTTGGCTATTTGAGTCGATCAGACCGCGCAGTGTGCGCTGGTCAGATCAGGGTTGTGCGGATGGTCAGATCAGGTAACTCAACGGTCTAA[C/T]
AGGTTAGCTCATGTATGGAGTTAGCTTCCAGCTGTTTAGTTGGATACTCATGATTACTTCATGTTATGACTTCTATATGATTACTATGCATATGTAATAC

Reverse complement sequence

GTATTACATATGCATAGTAATCATATAGAAGTCATAACATGAAGTAATCATGAGTATCCAACTAAACAGCTGGAAGCTAACTCCATACATGAGCTAACCT[G/A]
TTAGACCGTTGAGTTACCTGATCTGACCATCCGCACAACCCTGATCTGACCAGCGCACACTGCGCGGTCTGATCGACTCAAATAGCCAAAAAAAAAAACA

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 94.30% 1.80% 1.88% 2.03% NA
All Indica  2759 93.50% 2.80% 2.75% 0.94% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 70.60% 0.40% 3.35% 25.65% NA
Indica I  595 85.20% 6.70% 8.07% 0.00% NA
Indica II  465 98.50% 0.00% 1.29% 0.22% NA
Indica III  913 96.20% 2.80% 0.22% 0.77% NA
Indica Intermediate  786 93.60% 1.50% 2.54% 2.29% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 95.60% 1.10% 3.33% 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
vg0212130167 C -> T LOC_Os02g20560.1 upstream_gene_variant ; 905.0bp to feature; MODIFIER silent_mutation Average:57.569; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0212130167 C -> T LOC_Os02g20570.1 upstream_gene_variant ; 4085.0bp to feature; MODIFIER silent_mutation Average:57.569; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0212130167 C -> T LOC_Os02g20560-LOC_Os02g20570 intergenic_region ; MODIFIER silent_mutation Average:57.569; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N
vg0212130167 C -> DEL N N silent_mutation Average:57.569; most accessible tissue: Zhenshan97 flower, score: 70.106 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0212130167 NA 2.24E-06 mr1219 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
vg0212130167 NA 1.94E-09 mr1317 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
vg0212130167 NA 7.94E-10 mr1855 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
vg0212130167 NA 8.57E-06 mr1927 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
vg0212130167 NA 1.29E-06 mr1219_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
vg0212130167 NA 1.45E-07 mr1274_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
vg0212130167 NA 9.36E-10 mr1317_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
vg0212130167 NA 9.14E-08 mr1610_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
vg0212130167 NA 2.01E-08 mr1818_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
vg0212130167 2.22E-10 2.31E-20 mr1855_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
vg0212130167 6.82E-06 1.77E-09 mr1897_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
vg0212130167 4.22E-08 5.62E-15 mr1914_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
vg0212130167 NA 8.38E-11 mr1927_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