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Detailed information for vg1219170547:

Variant ID: vg1219170547 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19170547
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTTAATTACGAATTGAGGTATCATTAACTCATGCGGCAAAATATTTTTACCCAACTCGAATCAAAGACTTAGGTTGTGTTTAGTTCACACCAAAATT[A/G]
GAAGTTTGGTTGAAATTGGAACGATGTGTTGGAAAAGTTGAAAATTTGTGTGCGTAGAAAAGTTTTGATGTGATGGAAAAGTTGTAAGTTTGAAGAAAAA

Reverse complement sequence

TTTTTCTTCAAACTTACAACTTTTCCATCACATCAAAACTTTTCTACGCACACAAATTTTCAACTTTTCCAACACATCGTTCCAATTTCAACCAAACTTC[T/C]
AATTTTGGTGTGAACTAAACACAACCTAAGTCTTTGATTCGAGTTGGGTAAAAATATTTTGCCGCATGAGTTAATGATACCTCAATTCGTAATTAAAAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.30% 45.70% 0.04% 0.00% NA
All Indica  2759 23.50% 76.50% 0.04% 0.00% NA
All Japonica  1512 98.50% 1.50% 0.07% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 18.70% 81.20% 0.17% 0.00% NA
Indica II  465 35.70% 64.30% 0.00% 0.00% NA
Indica III  913 20.80% 79.20% 0.00% 0.00% NA
Indica Intermediate  786 22.90% 77.10% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 1.20% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg1219170547 A -> G LOC_Os12g31850.4 upstream_gene_variant ; 4127.0bp to feature; MODIFIER silent_mutation Average:31.197; most accessible tissue: Minghui63 flower, score: 41.625 N N N N
vg1219170547 A -> G LOC_Os12g31850-LOC_Os12g31860 intergenic_region ; MODIFIER silent_mutation Average:31.197; most accessible tissue: Minghui63 flower, score: 41.625 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219170547 NA 3.27E-06 mr1089 Ind_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
vg1219170547 NA 2.55E-07 mr1093 Ind_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
vg1219170547 NA 8.11E-31 mr1257 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
vg1219170547 NA 2.60E-06 mr1257 Ind_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
vg1219170547 NA 1.67E-06 mr1435 Ind_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
vg1219170547 NA 7.57E-07 mr1599 Ind_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
vg1219170547 NA 3.66E-09 mr1648 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