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Detailed information for vg0118782155:

Variant ID: vg0118782155 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18782155
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAGCTCGTCTTCGTCTGAGTCCATCTCGGGGCGATCTGCTGTCGAGATTGGGTGGCGGCCGGCAGGTGGGGGAAGCGGGAGGAGGGGATGGATGAGAGC[A/G]
TTGCGCCGCCGTGAGATGACAAGAGAGGTGAAGCGCGGAAGAGTGGTGGAGTGGTTCATGGGTCCCCCTCATCCTTCCGCTCCTCTGGCGAGTCCCTCCG

Reverse complement sequence

CGGAGGGACTCGCCAGAGGAGCGGAAGGATGAGGGGGACCCATGAACCACTCCACCACTCTTCCGCGCTTCACCTCTCTTGTCATCTCACGGCGGCGCAA[T/C]
GCTCTCATCCATCCCCTCCTCCCGCTTCCCCCACCTGCCGGCCGCCACCCAATCTCGACAGCAGATCGCCCCGAGATGGACTCAGACGAAGACGAGCTGC

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 47.20% 12.20% 1.29% 39.27% NA
All Indica  2759 32.10% 1.90% 2.10% 63.90% NA
All Japonica  1512 67.20% 28.00% 0.20% 4.63% NA
Aus  269 75.80% 23.40% 0.00% 0.74% NA
Indica I  595 45.00% 0.50% 0.00% 54.45% NA
Indica II  465 36.60% 1.50% 9.68% 52.26% NA
Indica III  913 18.00% 1.90% 0.33% 79.85% NA
Indica Intermediate  786 36.00% 3.30% 1.27% 59.41% NA
Temperate Japonica  767 84.60% 15.30% 0.00% 0.13% NA
Tropical Japonica  504 52.80% 33.90% 0.20% 13.10% NA
Japonica Intermediate  241 41.90% 56.00% 0.83% 1.24% NA
VI/Aromatic  96 72.90% 26.00% 0.00% 1.04% NA
Intermediate  90 62.20% 15.60% 0.00% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0118782155 A -> G LOC_Os01g34090.1 upstream_gene_variant ; 3968.0bp to feature; MODIFIER silent_mutation Average:40.498; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg0118782155 A -> G LOC_Os01g34110.1 upstream_gene_variant ; 115.0bp to feature; MODIFIER silent_mutation Average:40.498; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg0118782155 A -> G LOC_Os01g34100.1 downstream_gene_variant ; 763.0bp to feature; MODIFIER silent_mutation Average:40.498; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg0118782155 A -> G LOC_Os01g34100-LOC_Os01g34110 intergenic_region ; MODIFIER silent_mutation Average:40.498; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg0118782155 A -> DEL N N silent_mutation Average:40.498; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0118782155 2.95E-06 NA mr1035 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
vg0118782155 NA 5.86E-07 mr1622 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