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Detailed information for vg1125143652:

Variant ID: vg1125143652 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25143652
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.07, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TATTATTGAGGATGAGCGGCATGAGGAATTGTGATATGTCCTTTGGTCTAAGTCCTGCTGGTGCATATGTACTCTCAAGTCGCCACGATTTCACAGTGTA[A/G]
TTGTTCGATCCACACGTAGAACATGTTTATGATGGCAATTAACTAGAGTATTGCACATGTTTATGATGTCCTATTAACATGACATTTTAGGTGTTCCAGG

Reverse complement sequence

CCTGGAACACCTAAAATGTCATGTTAATAGGACATCATAAACATGTGCAATACTCTAGTTAATTGCCATCATAAACATGTTCTACGTGTGGATCGAACAA[T/C]
TACACTGTGAAATCGTGGCGACTTGAGAGTACATATGCACCAGCAGGACTTAGACCAAAGGACATATCACAATTCCTCATGCCGCTCATCCTCAATAATA

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 88.80% 11.10% 0.13% 0.00% NA
All Indica  2759 83.70% 16.30% 0.07% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 87.00% 12.30% 0.74% 0.00% NA
Indica I  595 96.60% 3.40% 0.00% 0.00% NA
Indica II  465 82.80% 17.00% 0.22% 0.00% NA
Indica III  913 78.20% 21.80% 0.00% 0.00% NA
Indica Intermediate  786 80.70% 19.20% 0.13% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 88.90% 8.90% 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
vg1125143652 A -> G LOC_Os11g41800-LOC_Os11g41820 intergenic_region ; MODIFIER silent_mutation Average:31.917; most accessible tissue: Zhenshan97 young leaf, score: 61.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125143652 8.96E-07 NA mr1133 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
vg1125143652 2.38E-06 2.38E-06 mr1487 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
vg1125143652 NA 2.76E-06 mr1133_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