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Detailed information for vg1114485144:

Variant ID: vg1114485144 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 14485144
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.33, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


GCATAAATGAGTTCAAAAACTGATCCCGTGTTTGCTGCAACGTTGCTTCAAACTCTTTCTTCTGTTCGGGTGTGAACTTTTCTGGATCGATTGGCATGAC[G/A]
TTCTTTTCAATGATGTCATCCAATCCCGACTTTGACGCCTTGTTTTTAGCAGAACCTGGGCTAGATGGTGGTGGAGGTTGTTTCTCGGCCATGAGGGAGA

Reverse complement sequence

TCTCCCTCATGGCCGAGAAACAACCTCCACCACCATCTAGCCCAGGTTCTGCTAAAAACAAGGCGTCAAAGTCGGGATTGGATGACATCATTGAAAAGAA[C/T]
GTCATGCCAATCGATCCAGAAAAGTTCACACCCGAACAGAAGAAAGAGTTTGAAGCAACGTTGCAGCAAACACGGGATCAGTTTTTGAACTCATTTATGC

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 45.40% 39.70% 1.33% 13.56% NA
All Indica  2759 65.30% 10.10% 2.17% 22.40% NA
All Japonica  1512 2.70% 96.90% 0.07% 0.33% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 71.80% 6.40% 1.18% 20.67% NA
Indica II  465 44.90% 15.70% 3.44% 35.91% NA
Indica III  913 72.70% 6.40% 2.41% 18.51% NA
Indica Intermediate  786 63.70% 14.10% 1.91% 20.23% NA
Temperate Japonica  767 3.00% 96.70% 0.13% 0.13% NA
Tropical Japonica  504 2.80% 96.60% 0.00% 0.60% NA
Japonica Intermediate  241 1.70% 97.90% 0.00% 0.41% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 28.90% 48.90% 2.22% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1114485144 G -> A LOC_Os11g25400.1 synonymous_variant ; p.Asn31Asn; LOW synonymous_codon Average:22.6; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 N N N N
vg1114485144 G -> DEL LOC_Os11g25400.1 N frameshift_variant Average:22.6; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1114485144 NA 8.51E-08 mr1084_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
vg1114485144 NA 9.81E-06 mr1272_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
vg1114485144 NA 7.89E-07 mr1275_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
vg1114485144 NA 1.15E-24 mr1350_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
vg1114485144 NA 6.32E-14 mr1529_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
vg1114485144 NA 8.06E-06 mr1574_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
vg1114485144 NA 6.96E-14 mr1575_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
vg1114485144 NA 6.29E-11 mr1835_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
vg1114485144 NA 3.58E-06 mr1835_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
vg1114485144 NA 1.75E-15 mr1904_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
vg1114485144 1.79E-06 2.62E-08 mr1904_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
vg1114485144 7.08E-06 NA mr1916_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