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Detailed information for vg1127164659:

Variant ID: vg1127164659 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27164659
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


AGATGGAACCAACCTATATATCTGGGAATCTTGAATTATGTCAGAATGGCACAGCATACACATTCTAACCTCTGAATCAAACAGCACTAATCTATGCAAT[G/A]
CAAAGAAAAAGCACTACTGAATCGCAGAAAATTTAATCCACCGAGGACACATCCCATCGATCGATTCGAAACATCATCAGCTCATGCATTTCACAATAGC

Reverse complement sequence

GCTATTGTGAAATGCATGAGCTGATGATGTTTCGAATCGATCGATGGGATGTGTCCTCGGTGGATTAAATTTTCTGCGATTCAGTAGTGCTTTTTCTTTG[C/T]
ATTGCATAGATTAGTGCTGTTTGATTCAGAGGTTAGAATGTGTATGCTGTGCCATTCTGACATAATTCAAGATTCCCAGATATATAGGTTGGTTCCATCT

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 70.40% 29.40% 0.19% 0.00% NA
All Indica  2759 82.50% 17.30% 0.18% 0.00% NA
All Japonica  1512 57.80% 42.10% 0.07% 0.00% NA
Aus  269 38.70% 61.00% 0.37% 0.00% NA
Indica I  595 74.30% 25.50% 0.17% 0.00% NA
Indica II  465 94.80% 4.90% 0.22% 0.00% NA
Indica III  913 86.60% 13.10% 0.22% 0.00% NA
Indica Intermediate  786 76.60% 23.30% 0.13% 0.00% NA
Temperate Japonica  767 66.20% 33.80% 0.00% 0.00% NA
Tropical Japonica  504 47.80% 52.00% 0.20% 0.00% NA
Japonica Intermediate  241 51.90% 48.10% 0.00% 0.00% NA
VI/Aromatic  96 17.70% 82.30% 0.00% 0.00% NA
Intermediate  90 64.40% 33.30% 2.22% 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
vg1127164659 G -> A LOC_Os11g44890.1 upstream_gene_variant ; 2882.0bp to feature; MODIFIER silent_mutation Average:41.997; most accessible tissue: Zhenshan97 root, score: 60.612 N N N N
vg1127164659 G -> A LOC_Os11g44880.1 intron_variant ; MODIFIER silent_mutation Average:41.997; most accessible tissue: Zhenshan97 root, score: 60.612 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127164659 6.63E-06 7.96E-07 mr1376 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
vg1127164659 NA 3.18E-08 mr1398 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
vg1127164659 6.63E-06 7.96E-07 mr1431 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
vg1127164659 NA 3.01E-06 mr1820 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
vg1127164659 NA 2.38E-06 mr1542_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