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Detailed information for vg0524661216:

Variant ID: vg0524661216 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 24661216
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCCGGGTGGCCGGTTGAAAAGCTGTTGGCCGGGTGCCAATCTTGTGTCATTTCTAAAGACTGATACATTGCACATACTCCGACCGGACGAGACGCACT[G/A]
TCTCATCCGCGTCGTTTGAGAAGCACTCACCTAGTTGTTTTTAGAAAAGAGTTCAAATAAAATCAATTGCAAAAACAACAGCCTTTCCTTGAAGCCTGCA

Reverse complement sequence

TGCAGGCTTCAAGGAAAGGCTGTTGTTTTTGCAATTGATTTTATTTGAACTCTTTTCTAAAAACAACTAGGTGAGTGCTTCTCAAACGACGCGGATGAGA[C/T]
AGTGCGTCTCGTCCGGTCGGAGTATGTGCAATGTATCAGTCTTTAGAAATGACACAAGATTGGCACCCGGCCAACAGCTTTTCAACCGGCCACCCGGGCC

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 99.80% 0.20% 0.04% 0.00% NA
All Indica  2759 99.70% 0.30% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0524661216 G -> A LOC_Os05g42170.1 upstream_gene_variant ; 2381.0bp to feature; MODIFIER N Average:36.505; most accessible tissue: Minghui63 root, score: 69.344 N N N N
vg0524661216 G -> A LOC_Os05g42180.1 upstream_gene_variant ; 2698.0bp to feature; MODIFIER N Average:36.505; most accessible tissue: Minghui63 root, score: 69.344 N N N N
vg0524661216 G -> A LOC_Os05g42170-LOC_Os05g42180 intergenic_region ; MODIFIER N Average:36.505; most accessible tissue: Minghui63 root, score: 69.344 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0524661216 9.20E-07 2.02E-06 mr1758 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