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Detailed information for vg0424638529:

Variant ID: vg0424638529 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24638529
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACACAAGTTACTTTTGAATGATTATATCATAATCGACGAAAATTGTATGCTTATATTATCGACAGTGGCAGATCGGGTTGGTTGGCTACTAATGACTTC[G/A]
TGCCTGTTTAGATGTCACCCTAAAATTTTTGCACCATATCACATCGAATGTTTAAACACCTACTTGAAGTATTAAATATAAGTTAAAAAAATAAGAATTG

Reverse complement sequence

CAATTCTTATTTTTTTAACTTATATTTAATACTTCAAGTAGGTGTTTAAACATTCGATGTGATATGGTGCAAAAATTTTAGGGTGACATCTAAACAGGCA[C/T]
GAAGTCATTAGTAGCCAACCAACCCGATCTGCCACTGTCGATAATATAAGCATACAATTTTCGTCGATTATGATATAATCATTCAAAAGTAACTTGTGTA

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 93.60% 6.10% 0.28% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 81.10% 18.10% 0.86% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 84.40% 15.10% 0.52% 0.00% NA
Tropical Japonica  504 77.20% 22.00% 0.79% 0.00% NA
Japonica Intermediate  241 78.80% 19.10% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0424638529 G -> A LOC_Os04g41540.1 upstream_gene_variant ; 1853.0bp to feature; MODIFIER silent_mutation Average:56.673; most accessible tissue: Callus, score: 74.584 N N N N
vg0424638529 G -> A LOC_Os04g41530.1 downstream_gene_variant ; 2689.0bp to feature; MODIFIER silent_mutation Average:56.673; most accessible tissue: Callus, score: 74.584 N N N N
vg0424638529 G -> A LOC_Os04g41530-LOC_Os04g41540 intergenic_region ; MODIFIER silent_mutation Average:56.673; most accessible tissue: Callus, score: 74.584 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0424638529 3.69E-06 NA mr1085 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
vg0424638529 NA 6.68E-06 mr1155 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
vg0424638529 1.33E-06 NA mr1226 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
vg0424638529 2.07E-06 NA mr1411 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
vg0424638529 3.24E-06 NA mr1437 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
vg0424638529 7.01E-06 NA mr1878 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
vg0424638529 8.40E-07 NA mr1082_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
vg0424638529 3.99E-06 NA mr1083_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
vg0424638529 3.48E-08 NA mr1104_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
vg0424638529 2.39E-06 NA mr1107_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
vg0424638529 2.06E-06 NA mr1226_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