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Detailed information for vg0628643421:

Variant ID: vg0628643421 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28643421
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATAAATCAAATGATAGGAAAAGAATTAATAATTACTTAAATTTTTTGAATAAGACAAATATTTAAACATTTTTAAAAAAATTAACGGCGTCAAATATTTA[A/G]
GGATAGAGGAAGTAGTAGAAAGGAGCAGTTTAACGATACTGTCACTGTGGGCGCCCACTTTACAGCGGCACGAGCTGCTGGTTCTGCATAGTAAGTCGTA

Reverse complement sequence

TACGACTTACTATGCAGAACCAGCAGCTCGTGCCGCTGTAAAGTGGGCGCCCACAGTGACAGTATCGTTAAACTGCTCCTTTCTACTACTTCCTCTATCC[T/C]
TAAATATTTGACGCCGTTAATTTTTTTAAAAATGTTTAAATATTTGTCTTATTCAAAAAATTTAAGTAATTATTAATTCTTTTCCTATCATTTGATTTAT

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 91.60% 6.20% 2.20% 0.00% NA
All Indica  2759 99.10% 0.20% 0.65% 0.00% NA
All Japonica  1512 75.80% 18.70% 5.56% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 1.00% 2.86% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 56.50% 35.10% 8.47% 0.00% NA
Tropical Japonica  504 98.00% 1.00% 0.99% 0.00% NA
Japonica Intermediate  241 90.90% 3.30% 5.81% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 6.70% 2.22% 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
vg0628643421 A -> G LOC_Os06g47230.1 upstream_gene_variant ; 2049.0bp to feature; MODIFIER silent_mutation Average:51.315; most accessible tissue: Callus, score: 78.667 N N N N
vg0628643421 A -> G LOC_Os06g47250.1 downstream_gene_variant ; 719.0bp to feature; MODIFIER silent_mutation Average:51.315; most accessible tissue: Callus, score: 78.667 N N N N
vg0628643421 A -> G LOC_Os06g47230-LOC_Os06g47250 intergenic_region ; MODIFIER silent_mutation Average:51.315; most accessible tissue: Callus, score: 78.667 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628643421 NA 5.70E-09 mr1010_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
vg0628643421 NA 4.29E-07 mr1051_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
vg0628643421 NA 2.63E-07 mr1446_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
vg0628643421 NA 3.76E-09 mr1576_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
vg0628643421 3.58E-06 NA mr1627_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
vg0628643421 NA 7.96E-10 mr1627_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
vg0628643421 1.12E-06 8.79E-09 mr1977_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
vg0628643421 1.15E-06 9.40E-07 mr1977_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