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Detailed information for vg0334741697:

Variant ID: vg0334741697 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 34741697
Reference Allele: GAlternative Allele: GT,T,GTT,GTTT
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTTTTTGTTTTTTTCTTCCTGCGCGTGTACGGTTTCTTTTTTTTTTCCGTTTTTTCTGTTTTCTTCCGTATTTTTGGTTTCTTTTTCCTTTGTTTTC[G/GT,T,GTT,GTTT]
TTTTTTTGTTTTCTCCCGTATTTTTGGTTTCTTTTTCTTTTTTTCTTTTTTATCGTTTTCAGTTTTTTTCGGTTTTTATAAAGTTTGTATACGTGTATAT

Reverse complement sequence

ATATACACGTATACAAACTTTATAAAAACCGAAAAAAACTGAAAACGATAAAAAAGAAAAAAAGAAAAAGAAACCAAAAATACGGGAGAAAACAAAAAAA[C/AC,A,AAC,AAAC]
GAAAACAAAGGAAAAAGAAACCAAAAATACGGAAGAAAACAGAAAAAACGGAAAAAAAAAAGAAACCGTACACGCGCAGGAAGAAAAAAACAAAAAAAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.10% 12.90% 6.52% 2.64% GT: 9.65%; GTT: 0.13%; GTTT: 0.02%
All Indica  2759 66.30% 5.90% 7.43% 4.31% GT: 16.02%; GTT: 0.04%
All Japonica  1512 71.00% 23.30% 5.42% 0.00% GT: 0.20%
Aus  269 87.00% 4.50% 3.72% 1.86% GT: 2.23%; GTT: 0.37%; GTTT: 0.37%
Indica I  595 78.50% 0.00% 16.64% 2.69% GT: 2.18%
Indica II  465 78.10% 1.30% 4.95% 6.67% GT: 9.03%
Indica III  913 50.80% 12.50% 2.96% 3.94% GT: 29.68%; GTT: 0.11%
Indica Intermediate  786 68.10% 5.50% 7.12% 4.58% GT: 14.76%
Temperate Japonica  767 90.40% 4.40% 5.08% 0.00% GT: 0.13%
Tropical Japonica  504 53.20% 41.90% 4.56% 0.00% GT: 0.40%
Japonica Intermediate  241 46.90% 44.80% 8.30% 0.00% NA
VI/Aromatic  96 20.80% 72.90% 2.08% 0.00% GTT: 4.17%
Intermediate  90 68.90% 14.40% 10.00% 1.11% GT: 5.56%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0334741697 G -> T LOC_Os03g61160.1 upstream_gene_variant ; 1067.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> T LOC_Os03g61160.2 upstream_gene_variant ; 1190.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> T LOC_Os03g61160.3 upstream_gene_variant ; 1190.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> T LOC_Os03g61160.5 upstream_gene_variant ; 1190.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> T LOC_Os03g61160.4 upstream_gene_variant ; 1042.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> T LOC_Os03g61170.1 downstream_gene_variant ; 1928.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> T LOC_Os03g61180.1 downstream_gene_variant ; 4398.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> T LOC_Os03g61160-LOC_Os03g61170 intergenic_region ; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GT LOC_Os03g61160.1 upstream_gene_variant ; 1068.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GT LOC_Os03g61160.2 upstream_gene_variant ; 1191.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GT LOC_Os03g61160.3 upstream_gene_variant ; 1191.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GT LOC_Os03g61160.5 upstream_gene_variant ; 1191.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GT LOC_Os03g61160.4 upstream_gene_variant ; 1043.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GT LOC_Os03g61170.1 downstream_gene_variant ; 1927.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GT LOC_Os03g61180.1 downstream_gene_variant ; 4397.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GT LOC_Os03g61160-LOC_Os03g61170 intergenic_region ; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTT LOC_Os03g61160.1 upstream_gene_variant ; 1068.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTT LOC_Os03g61160.2 upstream_gene_variant ; 1191.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTT LOC_Os03g61160.3 upstream_gene_variant ; 1191.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTT LOC_Os03g61160.5 upstream_gene_variant ; 1191.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTT LOC_Os03g61160.4 upstream_gene_variant ; 1043.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTT LOC_Os03g61170.1 downstream_gene_variant ; 1927.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTT LOC_Os03g61180.1 downstream_gene_variant ; 4397.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTT LOC_Os03g61160-LOC_Os03g61170 intergenic_region ; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> DEL N N silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTTT LOC_Os03g61160.1 upstream_gene_variant ; 1068.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTTT LOC_Os03g61160.2 upstream_gene_variant ; 1191.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTTT LOC_Os03g61160.3 upstream_gene_variant ; 1191.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTTT LOC_Os03g61160.5 upstream_gene_variant ; 1191.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTTT LOC_Os03g61160.4 upstream_gene_variant ; 1043.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTTT LOC_Os03g61170.1 downstream_gene_variant ; 1927.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTTT LOC_Os03g61180.1 downstream_gene_variant ; 4397.0bp to feature; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N
vg0334741697 G -> GTTT LOC_Os03g61160-LOC_Os03g61170 intergenic_region ; MODIFIER silent_mutation Average:66.259; most accessible tissue: Callus, score: 94.19 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334741697 9.70E-07 9.70E-07 mr1197_2 Jap_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