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Detailed information for vg0219154244:

Variant ID: vg0219154244 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19154244
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCAACGGTGTCAAACATTTTAAAACGGATGGAGTAGTTTACATTAAAAGAACTTAGCAATAAATATTAGTTTTAAACTTCCAATGATATTATTAAAGAG[C/A]
TAAAATTCAAGTTTTTCTTAAAGGACTAGTTTACGCATTGCTTGTTATTAGCGGTGACTATTTGACCTACTTTACTATTAATATTAGTTATTCAGTCTTA

Reverse complement sequence

TAAGACTGAATAACTAATATTAATAGTAAAGTAGGTCAAATAGTCACCGCTAATAACAAGCAATGCGTAAACTAGTCCTTTAAGAAAAACTTGAATTTTA[G/T]
CTCTTTAATAATATCATTGGAAGTTTAAAACTAATATTTATTGCTAAGTTCTTTTAATGTAAACTACTCCATCCGTTTTAAAATGTTTGACACCGTTGAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.50% 12.50% 0.06% 0.00% NA
All Indica  2759 86.30% 13.70% 0.07% 0.00% NA
All Japonica  1512 88.30% 11.70% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 94.60% 5.40% 0.00% 0.00% NA
Indica III  913 70.50% 29.40% 0.11% 0.00% NA
Indica Intermediate  786 89.60% 10.30% 0.13% 0.00% NA
Temperate Japonica  767 96.30% 3.70% 0.00% 0.00% NA
Tropical Japonica  504 78.60% 21.40% 0.00% 0.00% NA
Japonica Intermediate  241 83.00% 17.00% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 86.70% 12.20% 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
vg0219154244 C -> A LOC_Os02g32400.1 upstream_gene_variant ; 3587.0bp to feature; MODIFIER silent_mutation Average:49.476; most accessible tissue: Minghui63 panicle, score: 91.227 N N N N
vg0219154244 C -> A LOC_Os02g32390-LOC_Os02g32400 intergenic_region ; MODIFIER silent_mutation Average:49.476; most accessible tissue: Minghui63 panicle, score: 91.227 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219154244 NA 4.85E-06 mr1213 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
vg0219154244 1.78E-06 5.96E-07 mr1227 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
vg0219154244 NA 6.86E-06 mr1295 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
vg0219154244 NA 1.58E-08 mr1668 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
vg0219154244 NA 5.35E-10 mr1769 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
vg0219154244 NA 1.01E-07 mr1951 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