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Detailed information for vg1219727879:

Variant ID: vg1219727879 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19727879
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GCCACCAAGCCACATCAAATAATAGTTGACTACAAATAGATTGTGAGTATGAGTAATAGCATTCCTACACTCCTACAAATACTCCTAAGGCTGCGTTCGG[G/A]
AGTGAGGGTTCCCAACCCTCATTACCTGGCACGCAAAACGGAGCAGTATTTAGTGCGTGATTAATTAAGTATTAGCTAATTTTTTCTAAAAATAGATTAA

Reverse complement sequence

TTAATCTATTTTTAGAAAAAATTAGCTAATACTTAATTAATCACGCACTAAATACTGCTCCGTTTTGCGTGCCAGGTAATGAGGGTTGGGAACCCTCACT[C/T]
CCGAACGCAGCCTTAGGAGTATTTGTAGGAGTGTAGGAATGCTATTACTCATACTCACAATCTATTTGTAGTCAACTATTATTTGATGTGGCTTGGTGGC

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 78.40% 19.70% 1.86% 0.00% NA
All Indica  2759 64.00% 33.00% 3.01% 0.00% NA
All Japonica  1512 99.10% 0.70% 0.26% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 20.50% 75.80% 3.70% 0.00% NA
Indica II  465 75.50% 19.80% 4.73% 0.00% NA
Indica III  913 81.70% 16.30% 1.97% 0.00% NA
Indica Intermediate  786 69.60% 27.70% 2.67% 0.00% NA
Temperate Japonica  767 99.50% 0.40% 0.13% 0.00% NA
Tropical Japonica  504 99.00% 0.80% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 1.20% 0.83% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 90.00% 8.90% 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
vg1219727879 G -> A LOC_Os12g32680.1 downstream_gene_variant ; 2532.0bp to feature; MODIFIER silent_mutation Average:38.936; most accessible tissue: Minghui63 young leaf, score: 55.178 N N N N
vg1219727879 G -> A LOC_Os12g32670-LOC_Os12g32680 intergenic_region ; MODIFIER silent_mutation Average:38.936; most accessible tissue: Minghui63 young leaf, score: 55.178 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219727879 NA 9.60E-06 mr1215 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
vg1219727879 2.23E-06 NA mr1290 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
vg1219727879 NA 1.26E-09 mr1352 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
vg1219727879 5.73E-06 NA mr1420 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
vg1219727879 NA 6.23E-06 mr1502 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
vg1219727879 NA 1.59E-06 mr1886 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