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Detailed information for vg0819199007:

Variant ID: vg0819199007 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19199007
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCACACATATACTACGTAGACCAAAACCACCGCGGATTTGGTCGAGAGGGGTAATTCGTCCGGTTTGCATAGTTGGTGGTGAAGAATGTCCGGTTTTGTG[G/A]
TTTAGGGGGTAATTCGGACAACTACGATAGTTCGGGGGAGGGTAATTCGTACTTTTTCCTATTTAGTATCATGGCATTGCATGATTTGAAGAGTACGCAT

Reverse complement sequence

ATGCGTACTCTTCAAATCATGCAATGCCATGATACTAAATAGGAAAAAGTACGAATTACCCTCCCCCGAACTATCGTAGTTGTCCGAATTACCCCCTAAA[C/T]
CACAAAACCGGACATTCTTCACCACCAACTATGCAAACCGGACGAATTACCCCTCTCGACCAAATCCGCGGTGGTTTTGGTCTACGTAGTATATGTGTGG

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 89.30% 8.40% 2.24% 0.00% NA
All Indica  2759 98.20% 0.20% 1.56% 0.00% NA
All Japonica  1512 70.80% 25.10% 4.03% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 96.10% 0.10% 3.83% 0.00% NA
Indica Intermediate  786 99.00% 0.30% 0.76% 0.00% NA
Temperate Japonica  767 85.00% 9.00% 6.00% 0.00% NA
Tropical Japonica  504 43.50% 54.40% 2.18% 0.00% NA
Japonica Intermediate  241 83.00% 15.40% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 14.40% 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
vg0819199007 G -> A LOC_Os08g31080-LOC_Os08g31090 intergenic_region ; MODIFIER silent_mutation Average:62.112; most accessible tissue: Callus, score: 91.803 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819199007 NA 1.36E-09 mr1097 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
vg0819199007 NA 1.88E-07 mr1206 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
vg0819199007 NA 1.84E-06 mr1773 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