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Detailed information for vg1202107188:

Variant ID: vg1202107188 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2107188
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTCAGGAATATGGGTTGTAAGGTATTTATGCTTTTATTGTTATTATAAGTATGTATCTAATTTCCCCATTATTTTACCTCTATGTAAGTCCGTCTTAT[T/A]
TATTCGCTCTCATGCAAAATGATCTATGCATAAAATTTCGCTCTTATTCGATTCTGTTATTTGAGTCCTTTATTGCTTTATTTAATTTGGATTTGAGCAT

Reverse complement sequence

ATGCTCAAATCCAAATTAAATAAAGCAATAAAGGACTCAAATAACAGAATCGAATAAGAGCGAAATTTTATGCATAGATCATTTTGCATGAGAGCGAATA[A/T]
ATAAGACGGACTTACATAGAGGTAAAATAATGGGGAAATTAGATACATACTTATAATAACAATAAAAGCATAAATACCTTACAACCCATATTCCTGAGCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.00% 14.10% 1.84% 9.06% NA
All Indica  2759 60.90% 24.00% 2.68% 12.50% NA
All Japonica  1512 94.20% 0.10% 0.79% 4.89% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 25.50% 53.40% 3.70% 17.31% NA
Indica II  465 66.00% 12.50% 3.23% 18.28% NA
Indica III  913 78.80% 12.00% 1.75% 7.45% NA
Indica Intermediate  786 63.70% 22.30% 2.67% 11.32% NA
Temperate Japonica  767 95.70% 0.00% 0.65% 3.65% NA
Tropical Japonica  504 89.70% 0.40% 1.19% 8.73% NA
Japonica Intermediate  241 98.80% 0.00% 0.41% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 5.60% 0.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1202107188 T -> DEL N N silent_mutation Average:17.305; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 N N N N
vg1202107188 T -> A LOC_Os12g04900.1 upstream_gene_variant ; 131.0bp to feature; MODIFIER silent_mutation Average:17.305; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 N N N N
vg1202107188 T -> A LOC_Os12g04910.1 upstream_gene_variant ; 1337.0bp to feature; MODIFIER silent_mutation Average:17.305; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 N N N N
vg1202107188 T -> A LOC_Os12g04890.1 downstream_gene_variant ; 4555.0bp to feature; MODIFIER silent_mutation Average:17.305; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 N N N N
vg1202107188 T -> A LOC_Os12g04890-LOC_Os12g04900 intergenic_region ; MODIFIER silent_mutation Average:17.305; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202107188 1.38E-06 1.15E-42 mr1026 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
vg1202107188 NA 4.26E-21 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
vg1202107188 NA 2.42E-15 mr1118 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
vg1202107188 NA 6.13E-17 mr1118 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
vg1202107188 NA 4.89E-06 mr1120 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
vg1202107188 1.13E-06 1.69E-40 mr1161 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
vg1202107188 NA 8.35E-20 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
vg1202107188 NA 2.33E-06 mr1247 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
vg1202107188 NA 8.32E-06 mr1261 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
vg1202107188 NA 6.10E-17 mr1495 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
vg1202107188 NA 3.98E-07 mr1496 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
vg1202107188 NA 7.00E-08 mr1794 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
vg1202107188 NA 2.54E-19 mr1118_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
vg1202107188 8.25E-06 1.92E-23 mr1118_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
vg1202107188 NA 6.76E-08 mr1120_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
vg1202107188 3.42E-08 8.28E-44 mr1161_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
vg1202107188 1.12E-06 5.11E-23 mr1161_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
vg1202107188 NA 8.41E-07 mr1247_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
vg1202107188 NA 1.78E-25 mr1495_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
vg1202107188 4.20E-06 3.28E-23 mr1495_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
vg1202107188 NA 2.39E-08 mr1496_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
vg1202107188 NA 7.84E-07 mr1936_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