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Detailed information for vg0431983222:

Variant ID: vg0431983222 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31983222
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, T: 0.33, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCTGAAGCACAAAGCATCAGATCAAAATAACTCCCAGGTGGCATTTGTTGACAGTATACACCAAGGCAAAAACCCCCGATGAAAAATTTGGAGACAGT[T/G]
TTGTCTTATCTAGGATTGTTTTTTCGACTTGGGCATAAAAAACCGTAACTAGATCTCCTCTTTGCAGCATTTAATGACCCAACAAAGGAGTTAGATAAAG

Reverse complement sequence

CTTTATCTAACTCCTTTGTTGGGTCATTAAATGCTGCAAAGAGGAGATCTAGTTACGGTTTTTTATGCCCAAGTCGAAAAAACAATCCTAGATAAGACAA[A/C]
ACTGTCTCCAAATTTTTCATCGGGGGTTTTTGCCTTGGTGTATACTGTCAACAAATGCCACCTGGGAGTTATTTTGATCTGATGCTTTGTGCTTCAGCAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.30% 20.70% 0.00% 0.00% NA
All Indica  2759 87.20% 12.80% 0.00% 0.00% NA
All Japonica  1512 65.10% 34.90% 0.00% 0.00% NA
Aus  269 82.20% 17.80% 0.00% 0.00% NA
Indica I  595 87.20% 12.80% 0.00% 0.00% NA
Indica II  465 78.90% 21.10% 0.00% 0.00% NA
Indica III  913 89.00% 11.00% 0.00% 0.00% NA
Indica Intermediate  786 90.10% 9.90% 0.00% 0.00% NA
Temperate Japonica  767 48.10% 51.90% 0.00% 0.00% NA
Tropical Japonica  504 89.30% 10.70% 0.00% 0.00% NA
Japonica Intermediate  241 68.90% 31.10% 0.00% 0.00% NA
VI/Aromatic  96 65.60% 34.40% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0431983222 T -> G LOC_Os04g53660.1 upstream_gene_variant ; 2064.0bp to feature; MODIFIER silent_mutation Average:41.355; most accessible tissue: Callus, score: 55.908 N N N N
vg0431983222 T -> G LOC_Os04g53660.3 upstream_gene_variant ; 2064.0bp to feature; MODIFIER silent_mutation Average:41.355; most accessible tissue: Callus, score: 55.908 N N N N
vg0431983222 T -> G LOC_Os04g53660.2 upstream_gene_variant ; 2064.0bp to feature; MODIFIER silent_mutation Average:41.355; most accessible tissue: Callus, score: 55.908 N N N N
vg0431983222 T -> G LOC_Os04g53670.1 intron_variant ; MODIFIER silent_mutation Average:41.355; most accessible tissue: Callus, score: 55.908 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431983222 1.23E-06 NA mr1122 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
vg0431983222 NA 4.71E-07 mr1411 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