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Detailed information for vg0526394533:

Variant ID: vg0526394533 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 26394533
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACGGTATTTTGTACTCCCTCCGTTTCGTTTTATCTGACACCGTTGACTTTTTAGCACATGTTTGACCGTTCGTTTTATTCAAAAACTTTTGTGAAATAT[G/A]
TAAAACTATACGCATGCATAAAAGTATATTTACCAATGAATCAAATGATAGGAAAATAATTAATAATTATTTAAATTTTTTGAATAAGATGAGCGGTCAA

Reverse complement sequence

TTGACCGCTCATCTTATTCAAAAAATTTAAATAATTATTAATTATTTTCCTATCATTTGATTCATTGGTAAATATACTTTTATGCATGCGTATAGTTTTA[C/T]
ATATTTCACAAAAGTTTTTGAATAAAACGAACGGTCAAACATGTGCTAAAAAGTCAACGGTGTCAGATAAAACGAAACGGAGGGAGTACAAAATACCGTC

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 93.00% 3.90% 1.02% 2.09% NA
All Indica  2759 98.00% 0.80% 1.09% 0.07% NA
All Japonica  1512 92.90% 0.00% 0.73% 6.42% NA
Aus  269 39.00% 59.10% 1.86% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.10% 0.90% 1.08% 0.00% NA
Indica III  913 97.00% 0.40% 2.41% 0.11% NA
Indica Intermediate  786 97.60% 1.90% 0.38% 0.13% NA
Temperate Japonica  767 97.80% 0.00% 0.13% 2.09% NA
Tropical Japonica  504 92.50% 0.00% 0.99% 6.55% NA
Japonica Intermediate  241 78.00% 0.00% 2.07% 19.92% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 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
vg0526394533 G -> DEL N N silent_mutation Average:67.776; most accessible tissue: Zhenshan97 flower, score: 92.109 N N N N
vg0526394533 G -> A LOC_Os05g45520.1 upstream_gene_variant ; 3259.0bp to feature; MODIFIER silent_mutation Average:67.776; most accessible tissue: Zhenshan97 flower, score: 92.109 N N N N
vg0526394533 G -> A LOC_Os05g45530.1 upstream_gene_variant ; 512.0bp to feature; MODIFIER silent_mutation Average:67.776; most accessible tissue: Zhenshan97 flower, score: 92.109 N N N N
vg0526394533 G -> A LOC_Os05g45540.1 downstream_gene_variant ; 2787.0bp to feature; MODIFIER silent_mutation Average:67.776; most accessible tissue: Zhenshan97 flower, score: 92.109 N N N N
vg0526394533 G -> A LOC_Os05g45550.1 downstream_gene_variant ; 4573.0bp to feature; MODIFIER silent_mutation Average:67.776; most accessible tissue: Zhenshan97 flower, score: 92.109 N N N N
vg0526394533 G -> A LOC_Os05g45520-LOC_Os05g45530 intergenic_region ; MODIFIER silent_mutation Average:67.776; most accessible tissue: Zhenshan97 flower, score: 92.109 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0526394533 3.08E-06 NA mr1261 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