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Detailed information for vg0624773677:

Variant ID: vg0624773677 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24773677
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATATATATATATATATTTACAATCAAGCTACGAGGAAAAAAATAAAACATCATAGTATAGTTTATCAGTACTTATCATATGAAATAAACAAATGATAC[C/T]
GCACTTTAATATGAAACAAATTTTTTAGGGGTAATGTTAAATATTACAAAAATAATATATGGATTTGTTACAATATTATGAAAATAATATGAGGGGTGAT

Reverse complement sequence

ATCACCCCTCATATTATTTTCATAATATTGTAACAAATCCATATATTATTTTTGTAATATTTAACATTACCCCTAAAAAATTTGTTTCATATTAAAGTGC[G/A]
GTATCATTTGTTTATTTCATATGATAAGTACTGATAAACTATACTATGATGTTTTATTTTTTTCCTCGTAGCTTGATTGTAAATATATATATATATATAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.60% 3.40% 0.02% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 90.20% 9.70% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 72.60% 27.20% 0.20% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0624773677 C -> T LOC_Os06g41350.1 downstream_gene_variant ; 4070.0bp to feature; MODIFIER silent_mutation Average:29.321; most accessible tissue: Callus, score: 58.494 N N N N
vg0624773677 C -> T LOC_Os06g41350-LOC_Os06g41360 intergenic_region ; MODIFIER silent_mutation Average:29.321; most accessible tissue: Callus, score: 58.494 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624773677 NA 3.24E-07 mr1583 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
vg0624773677 NA 2.89E-06 mr1682 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
vg0624773677 9.47E-07 9.47E-07 mr1848 Jap_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
vg0624773677 1.31E-06 8.91E-08 mr1850_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