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Detailed information for vg1226265159:

Variant ID: vg1226265159 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 26265159
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.21, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


TGTAAAATTAAAGGTGTTTTTGATTATTATTCTGTGATGAATAATTGGGCATTGGAGATTATTGGTTTTGTTATTTGGAATTTATTTACGAAGTGGTTTT[A/G]
GAGATGATTGGATTTACAGGTGAATCGCAGGTTCATTATTTCATGTGACCGGTCAGACCGGGCAGTGTGTGCCGGTCAGACCGGCGGTGATCGAGCGGTC

Reverse complement sequence

GACCGCTCGATCACCGCCGGTCTGACCGGCACACACTGCCCGGTCTGACCGGTCACATGAAATAATGAACCTGCGATTCACCTGTAAATCCAATCATCTC[T/C]
AAAACCACTTCGTAAATAAATTCCAAATAACAAAACCAATAATCTCCAATGCCCAATTATTCATCACAGAATAATAATCAAAAACACCTTTAATTTTACA

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 56.20% 42.90% 0.91% 0.00% NA
All Indica  2759 35.00% 63.90% 1.05% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 13.40% 82.90% 3.72% 0.00% NA
Indica I  595 10.10% 87.90% 2.02% 0.00% NA
Indica II  465 34.60% 64.70% 0.65% 0.00% NA
Indica III  913 52.60% 46.80% 0.66% 0.00% NA
Indica Intermediate  786 33.70% 65.30% 1.02% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 66.70% 28.90% 4.44% 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
vg1226265159 A -> G LOC_Os12g42280.1 upstream_gene_variant ; 3071.0bp to feature; MODIFIER silent_mutation Average:35.724; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg1226265159 A -> G LOC_Os12g42270-LOC_Os12g42280 intergenic_region ; MODIFIER silent_mutation Average:35.724; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1226265159 NA 1.50E-23 mr1168 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
vg1226265159 NA 2.08E-06 mr1278 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
vg1226265159 NA 2.87E-10 mr1302 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
vg1226265159 NA 1.56E-10 mr1307 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
vg1226265159 NA 1.13E-06 mr1315 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
vg1226265159 NA 6.26E-07 mr1392 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
vg1226265159 NA 3.02E-09 mr1488 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
vg1226265159 NA 2.71E-06 mr1508 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
vg1226265159 NA 9.29E-11 mr1775 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
vg1226265159 NA 2.40E-08 mr1776 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
vg1226265159 NA 8.77E-08 mr1810 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
vg1226265159 NA 8.06E-07 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
vg1226265159 NA 1.41E-09 mr1986 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
vg1226265159 NA 6.49E-08 mr1004_2 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
vg1226265159 8.59E-06 NA mr1744_2 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
vg1226265159 5.49E-08 5.49E-08 mr1744_2 Ind_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