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Detailed information for vg1118868501:

Variant ID: vg1118868501 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 18868501
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


ACATACCACGTAGCGGGTTGACGCAGTCACCCACACACCCCAGTCATGTCCATGCCTTTTCTTGATGAGGGCACCGGGCCCTATAAAAGATACCACGGAA[G/A]
TAGTTCGCCTGCGTGGCGAGTTGAGGCTACTCACCACATAGGTGCATTGTGTATAGCCTTACATACTGATTTGTATATTAGTTCTTTTCACTTGATTTAT

Reverse complement sequence

ATAAATCAAGTGAAAAGAACTAATATACAAATCAGTATGTAAGGCTATACACAATGCACCTATGTGGTGAGTAGCCTCAACTCGCCACGCAGGCGAACTA[C/T]
TTCCGTGGTATCTTTTATAGGGCCCGGTGCCCTCATCAAGAAAAGGCATGGACATGACTGGGGTGTGTGGGTGACTGCGTCAACCCGCTACGTGGTATGT

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 94.80% 5.10% 0.11% 0.00% NA
All Indica  2759 91.20% 8.70% 0.18% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 91.60% 8.20% 0.22% 0.00% NA
Indica III  913 86.60% 12.90% 0.44% 0.00% NA
Indica Intermediate  786 90.50% 9.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg1118868501 G -> A LOC_Os11g32010.1 downstream_gene_variant ; 226.0bp to feature; MODIFIER silent_mutation Average:70.64; most accessible tissue: Zhenshan97 young leaf, score: 88.513 N N N N
vg1118868501 G -> A LOC_Os11g32020.1 downstream_gene_variant ; 2361.0bp to feature; MODIFIER silent_mutation Average:70.64; most accessible tissue: Zhenshan97 young leaf, score: 88.513 N N N N
vg1118868501 G -> A LOC_Os11g32010-LOC_Os11g32020 intergenic_region ; MODIFIER silent_mutation Average:70.64; most accessible tissue: Zhenshan97 young leaf, score: 88.513 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1118868501 4.89E-06 NA mr1935 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
vg1118868501 NA 6.13E-06 mr1138_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
vg1118868501 NA 3.91E-07 mr1354_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