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Detailed information for vg0417591285:

Variant ID: vg0417591285 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 17591285
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTATGGGCTGTAGGTTTCTCACACCAATTGGATGAATTAGATCTAAAAATTAGAGGAGAGCATGATTGGATTGCACGCAATTCATTGTTCAAAAGGCACA[A/G]
TTGGTTGGATAGGAGTACAATGCTGCTAAGAATAATTGTTTTCTTTTTAAATAACCTATGGCTGAAAATTATGATCTTGAATGCTAAAGGATAATGCGAT

Reverse complement sequence

ATCGCATTATCCTTTAGCATTCAAGATCATAATTTTCAGCCATAGGTTATTTAAAAAGAAAACAATTATTCTTAGCAGCATTGTACTCCTATCCAACCAA[T/C]
TGTGCCTTTTGAACAATGAATTGCGTGCAATCCAATCATGCTCTCCTCTAATTTTTAGATCTAATTCATCCAATTGGTGTGAGAAACCTACAGCCCATAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.50% 11.50% 0.04% 0.00% NA
All Indica  2759 94.80% 5.20% 0.00% 0.00% NA
All Japonica  1512 74.80% 25.10% 0.07% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 79.00% 21.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 57.40% 42.50% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 78.80% 21.20% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 1.11% 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
vg0417591285 A -> G LOC_Os04g29580.1 downstream_gene_variant ; 1531.0bp to feature; MODIFIER silent_mutation Average:39.118; most accessible tissue: Callus, score: 65.996 N N N N
vg0417591285 A -> G LOC_Os04g29590.1 downstream_gene_variant ; 2906.0bp to feature; MODIFIER silent_mutation Average:39.118; most accessible tissue: Callus, score: 65.996 N N N N
vg0417591285 A -> G LOC_Os04g29580-LOC_Os04g29590 intergenic_region ; MODIFIER silent_mutation Average:39.118; most accessible tissue: Callus, score: 65.996 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0417591285 NA 4.98E-06 mr1648 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
vg0417591285 NA 7.48E-06 mr1066_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
vg0417591285 6.37E-07 NA mr1617_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
vg0417591285 NA 5.51E-08 mr1659_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
vg0417591285 NA 3.61E-07 mr1807_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