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Detailed information for vg1217551737:

Variant ID: vg1217551737 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17551737
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


GAATTAAACACTGTGGGTTGTGTTTTTTCCAACATTTAGCTCTGTTTAAGCTGAAACCGAGAGTTGATTACAGAATAATTATAATGTATCGTGTTATGTC[A/G]
TATTTGGATTTTGTACTATTTATTCATATAGGTGAAAGAAATTATTATATTATAAATCTGAGCACAATATTAACGAATATCAAGAGAACTCTTACAAAGA

Reverse complement sequence

TCTTTGTAAGAGTTCTCTTGATATTCGTTAATATTGTGCTCAGATTTATAATATAATAATTTCTTTCACCTATATGAATAAATAGTACAAAATCCAAATA[T/C]
GACATAACACGATACATTATAATTATTCTGTAATCAACTCTCGGTTTCAGCTTAAACAGAGCTAAATGTTGGAAAAAACACAACCCACAGTGTTTAATTC

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 64.20% 20.00% 0.83% 14.92% NA
All Indica  2759 89.40% 8.80% 0.58% 1.20% NA
All Japonica  1512 14.90% 44.00% 0.66% 40.48% NA
Aus  269 91.40% 4.10% 0.37% 4.09% NA
Indica I  595 88.40% 8.70% 1.18% 1.68% NA
Indica II  465 90.80% 9.00% 0.00% 0.22% NA
Indica III  913 88.60% 10.30% 0.55% 0.55% NA
Indica Intermediate  786 90.20% 7.10% 0.51% 2.16% NA
Temperate Japonica  767 1.70% 77.30% 0.65% 20.34% NA
Tropical Japonica  504 27.80% 1.40% 0.40% 70.44% NA
Japonica Intermediate  241 29.90% 27.00% 1.24% 41.91% NA
VI/Aromatic  96 50.00% 1.00% 9.38% 39.58% NA
Intermediate  90 56.70% 27.80% 3.33% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1217551737 A -> DEL N N silent_mutation Average:17.764; most accessible tissue: Minghui63 young leaf, score: 21.268 N N N N
vg1217551737 A -> G LOC_Os12g29510-LOC_Os12g29520 intergenic_region ; MODIFIER silent_mutation Average:17.764; most accessible tissue: Minghui63 young leaf, score: 21.268 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217551737 NA 1.15E-10 mr1198 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
vg1217551737 NA 7.29E-13 mr1239 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
vg1217551737 NA 9.51E-09 mr1275 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
vg1217551737 NA 1.63E-06 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
vg1217551737 NA 2.61E-06 mr1443 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
vg1217551737 6.59E-06 NA mr1458 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
vg1217551737 7.72E-07 2.02E-09 mr1458 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
vg1217551737 8.90E-06 NA mr1536 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
vg1217551737 1.86E-06 1.86E-06 mr1564 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
vg1217551737 NA 4.07E-06 mr1578 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
vg1217551737 NA 1.19E-12 mr1641 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
vg1217551737 NA 9.99E-10 mr1659 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
vg1217551737 2.12E-06 4.48E-09 mr1819 Jap_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
vg1217551737 NA 1.22E-09 mr1866 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
vg1217551737 NA 1.04E-06 mr1457_2 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
vg1217551737 8.14E-07 NA mr1458_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
vg1217551737 5.79E-10 5.25E-16 mr1458_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
vg1217551737 NA 7.68E-06 mr1577_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