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Detailed information for vg0402345102:

Variant ID: vg0402345102 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2345102
Reference Allele: AAlternative Allele: T,C
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGATACAATGTACCGATGATAAGCACCTTCCCTTTTTGTTTACGGCAGTGCCTTGTATGCGCGTAATAAGGGAGAAATGTGTAATACAGACAAGTTCTA[A/T,C]
GAGGATTCTTTTGGAAGATGCGGATATATGATCATGTGTATAATTGTTTACTGACAAAGGAGACCTAGGGTCTCGTGTCAGAGGAACTATGTTCTAACCT

Reverse complement sequence

AGGTTAGAACATAGTTCCTCTGACACGAGACCCTAGGTCTCCTTTGTCAGTAAACAATTATACACATGATCATATATCCGCATCTTCCAAAAGAATCCTC[T/A,G]
TAGAACTTGTCTGTATTACACATTTCTCCCTTATTACGCGCATACAAGGCACTGCCGTAAACAAAAAGGGAAGGTGCTTATCATCGGTACATTGTATCCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.40% 7.90% 5.50% 3.83% C: 1.35%
All Indica  2759 78.70% 12.60% 7.21% 1.27% C: 0.18%
All Japonica  1512 88.70% 0.20% 2.38% 4.83% C: 3.90%
Aus  269 75.10% 4.10% 7.43% 13.38% NA
Indica I  595 95.10% 1.70% 1.34% 1.85% NA
Indica II  465 80.40% 10.50% 8.60% 0.22% C: 0.22%
Indica III  913 64.10% 23.50% 9.75% 2.19% C: 0.44%
Indica Intermediate  786 82.20% 9.50% 7.89% 0.38% NA
Temperate Japonica  767 94.50% 0.10% 2.09% 1.96% C: 1.30%
Tropical Japonica  504 82.90% 0.20% 1.98% 6.15% C: 8.73%
Japonica Intermediate  241 82.20% 0.40% 4.15% 11.20% C: 2.07%
VI/Aromatic  96 59.40% 4.20% 2.08% 34.38% NA
Intermediate  90 84.40% 7.80% 3.33% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402345102 A -> C LOC_Os04g04880.1 upstream_gene_variant ; 4157.0bp to feature; MODIFIER silent_mutation Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0402345102 A -> C LOC_Os04g04860.1 downstream_gene_variant ; 558.0bp to feature; MODIFIER silent_mutation Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0402345102 A -> C LOC_Os04g04870.1 downstream_gene_variant ; 2418.0bp to feature; MODIFIER silent_mutation Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0402345102 A -> C LOC_Os04g04860-LOC_Os04g04870 intergenic_region ; MODIFIER silent_mutation Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0402345102 A -> DEL N N silent_mutation Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0402345102 A -> T LOC_Os04g04880.1 upstream_gene_variant ; 4157.0bp to feature; MODIFIER silent_mutation Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0402345102 A -> T LOC_Os04g04860.1 downstream_gene_variant ; 558.0bp to feature; MODIFIER silent_mutation Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0402345102 A -> T LOC_Os04g04870.1 downstream_gene_variant ; 2418.0bp to feature; MODIFIER silent_mutation Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N
vg0402345102 A -> T LOC_Os04g04860-LOC_Os04g04870 intergenic_region ; MODIFIER silent_mutation Average:17.378; most accessible tissue: Zhenshan97 flag leaf, score: 37.1 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402345102 1.20E-07 NA mr1022_2 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