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Detailed information for vg1203906173:

Variant ID: vg1203906173 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3906173
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


ACTGGCTCCCCTTCTATTCGGTGGGGTATTTTTCGTGACTTTGAGTATGATAGTCCCTCTTGCCCTGTTTTCACCAGACGTCTCCGGTTACTTTAGGGGC[A/G]
TGAGGAGCCGAAGTTTCTTGTCCAATTCTTTTTGTTCGAGGCCTCTAGACAAGACGAGGGGTACCTTTACTTTCTTCGGTATCACCCTTCTCCGGTGCAT

Reverse complement sequence

ATGCACCGGAGAAGGGTGATACCGAAGAAAGTAAAGGTACCCCTCGTCTTGTCTAGAGGCCTCGAACAAAAAGAATTGGACAAGAAACTTCGGCTCCTCA[T/C]
GCCCCTAAAGTAACCGGAGACGTCTGGTGAAAACAGGGCAAGAGGGACTATCATACTCAAAGTCACGAAAAATACCCCACCGAATAGAAGGGGAGCCAGT

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 97.40% 2.30% 0.34% 0.00% NA
All Indica  2759 96.70% 2.90% 0.36% 0.00% NA
All Japonica  1512 98.80% 1.00% 0.20% 0.00% NA
Aus  269 96.70% 3.00% 0.37% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 94.80% 4.30% 0.86% 0.00% NA
Indica III  913 95.80% 3.70% 0.44% 0.00% NA
Indica Intermediate  786 96.60% 3.20% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 97.00% 2.40% 0.60% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 2.10% 1.04% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg1203906173 A -> G LOC_Os12g07760.1 upstream_gene_variant ; 2963.0bp to feature; MODIFIER silent_mutation Average:22.221; most accessible tissue: Zhenshan97 root, score: 43.05 N N N N
vg1203906173 A -> G LOC_Os12g07750-LOC_Os12g07760 intergenic_region ; MODIFIER silent_mutation Average:22.221; most accessible tissue: Zhenshan97 root, score: 43.05 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203906173 9.23E-07 9.11E-07 mr1425 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