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Detailed information for vg1104344322:

Variant ID: vg1104344322 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 4344322
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.26, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


CGAAAATGTTTCAATCGTTTAAATCGGGCGTTGTTTCACTTTATATAAAAACAATGTTTCAGCAAATATGGAAAGAATGTTTCAATTCACTGGAACATTT[A/G]
ATCCATACATAGTGAAACATTATAAGTACACTAAGTGAAACATTTTTTGGTAGAACAAAAAAAATAAAACGAATTCTCTTAATAGAGGGTTTCCAAAATA

Reverse complement sequence

TATTTTGGAAACCCTCTATTAAGAGAATTCGTTTTATTTTTTTTGTTCTACCAAAAAATGTTTCACTTAGTGTACTTATAATGTTTCACTATGTATGGAT[T/C]
AAATGTTCCAGTGAATTGAAACATTCTTTCCATATTTGCTGAAACATTGTTTTTATATAAAGTGAAACAACGCCCGATTTAAACGATTGAAACATTTTCG

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 60.60% 39.30% 0.08% 0.00% NA
All Indica  2759 90.10% 9.70% 0.11% 0.00% NA
All Japonica  1512 15.10% 84.90% 0.00% 0.00% NA
Aus  269 22.70% 77.30% 0.00% 0.00% NA
Indica I  595 79.70% 20.00% 0.34% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 94.20% 5.80% 0.00% 0.00% NA
Indica Intermediate  786 89.70% 10.20% 0.13% 0.00% NA
Temperate Japonica  767 2.90% 97.10% 0.00% 0.00% NA
Tropical Japonica  504 34.10% 65.90% 0.00% 0.00% NA
Japonica Intermediate  241 14.10% 85.90% 0.00% 0.00% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 62.20% 36.70% 1.11% 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
vg1104344322 A -> G LOC_Os11g08285.1 upstream_gene_variant ; 1531.0bp to feature; MODIFIER silent_mutation Average:19.652; most accessible tissue: Callus, score: 29.104 N N N N
vg1104344322 A -> G LOC_Os11g08280.1 downstream_gene_variant ; 1507.0bp to feature; MODIFIER silent_mutation Average:19.652; most accessible tissue: Callus, score: 29.104 N N N N
vg1104344322 A -> G LOC_Os11g08280-LOC_Os11g08285 intergenic_region ; MODIFIER silent_mutation Average:19.652; most accessible tissue: Callus, score: 29.104 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1104344322 1.45E-07 1.45E-07 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
vg1104344322 7.96E-06 NA mr1549 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
vg1104344322 1.08E-12 1.60E-40 mr1638 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
vg1104344322 6.07E-12 3.75E-14 mr1638 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