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Detailed information for vg0325722534:

Variant ID: vg0325722534 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 25722534
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TGAGGCAAATACAATAGAATACAATTTTTTAAAATGTATATATTTTTCAAAGAGTGGAACAAATAATTTATATACTTGTTTTAATAATCTCTACTCGCTC[C/A,T]
ATCCGCAAATATAAGAGATTTTAAGTGGATGTGACACTCATAGTACAATGAATCTGGACATATTTTATGTCCATATTCATTGTACAGGAATAGAAAATCT

Reverse complement sequence

AGATTTTCTATTCCTGTACAATGAATATGGACATAAAATATGTCCAGATTCATTGTACTATGAGTGTCACATCCACTTAAAATCTCTTATATTTGCGGAT[G/T,A]
GAGCGAGTAGAGATTATTAAAACAAGTATATAAATTATTTGTTCCACTCTTTGAAAAATATATACATTTTAAAAAATTGTATTCTATTGTATTTGCCTCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 2.40% 1.29% 0.44% T: 0.02%
All Indica  2759 93.80% 4.00% 2.14% 0.00% T: 0.04%
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 99.30% 0.00% 0.00% 0.74% NA
Indica I  595 83.90% 9.90% 6.22% 0.00% NA
Indica II  465 96.30% 3.00% 0.65% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 92.60% 4.80% 2.42% 0.00% T: 0.13%
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 83.30% 0.00% 0.00% 16.67% NA
Intermediate  90 95.60% 0.00% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0325722534 C -> T LOC_Os03g45570.1 upstream_gene_variant ; 270.0bp to feature; MODIFIER silent_mutation Average:32.723; most accessible tissue: Callus, score: 68.365 N N N N
vg0325722534 C -> T LOC_Os03g45580.1 upstream_gene_variant ; 2548.0bp to feature; MODIFIER silent_mutation Average:32.723; most accessible tissue: Callus, score: 68.365 N N N N
vg0325722534 C -> T LOC_Os03g45590.1 upstream_gene_variant ; 4376.0bp to feature; MODIFIER silent_mutation Average:32.723; most accessible tissue: Callus, score: 68.365 N N N N
vg0325722534 C -> T LOC_Os03g45570-LOC_Os03g45580 intergenic_region ; MODIFIER silent_mutation Average:32.723; most accessible tissue: Callus, score: 68.365 N N N N
vg0325722534 C -> A LOC_Os03g45570.1 upstream_gene_variant ; 270.0bp to feature; MODIFIER silent_mutation Average:32.723; most accessible tissue: Callus, score: 68.365 N N N N
vg0325722534 C -> A LOC_Os03g45580.1 upstream_gene_variant ; 2548.0bp to feature; MODIFIER silent_mutation Average:32.723; most accessible tissue: Callus, score: 68.365 N N N N
vg0325722534 C -> A LOC_Os03g45590.1 upstream_gene_variant ; 4376.0bp to feature; MODIFIER silent_mutation Average:32.723; most accessible tissue: Callus, score: 68.365 N N N N
vg0325722534 C -> A LOC_Os03g45570-LOC_Os03g45580 intergenic_region ; MODIFIER silent_mutation Average:32.723; most accessible tissue: Callus, score: 68.365 N N N N
vg0325722534 C -> DEL N N silent_mutation Average:32.723; most accessible tissue: Callus, score: 68.365 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0325722534 NA 1.04E-07 Spikelet_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0325722534 1.11E-08 2.82E-14 mr1038 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
vg0325722534 1.28E-07 5.50E-14 mr1038 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
vg0325722534 2.43E-08 1.39E-15 mr1389 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
vg0325722534 2.22E-07 5.62E-14 mr1389 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
vg0325722534 NA 1.43E-06 mr1553 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
vg0325722534 3.98E-11 2.41E-19 mr1038_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
vg0325722534 1.12E-09 2.18E-17 mr1038_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
vg0325722534 NA 3.84E-06 mr1045_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
vg0325722534 2.04E-08 NA mr1141_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
vg0325722534 1.93E-07 NA mr1141_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
vg0325722534 NA 1.06E-06 mr1359_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
vg0325722534 NA 4.58E-07 mr1359_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
vg0325722534 NA 2.24E-06 mr1378_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
vg0325722534 1.06E-11 1.31E-16 mr1389_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
vg0325722534 3.49E-10 8.91E-16 mr1389_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
vg0325722534 NA 6.52E-06 mr1520_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
vg0325722534 NA 3.10E-08 mr1968_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