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Detailed information for vg1207844031:

Variant ID: vg1207844031 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7844031
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTCGTCGCGTGGTGGTAAGGATCCCTCTCCCTCGCTGCCCCGTCCTCGTCCTTTCGGTGTCGCCCGTGCCCGTTGTGCGGTTGTCGGCCCCGGTACCC[A/G]
TGTATCGGTGTCGGCAGTCGTTCGCTTGTGCGTGTGGTGACCGTGTTAGTGTGTCCGCTCGGTAGCCGCGTGGTTTCCACGTGTGCAGCCCGTGTGGTGT

Reverse complement sequence

ACACCACACGGGCTGCACACGTGGAAACCACGCGGCTACCGAGCGGACACACTAACACGGTCACCACACGCACAAGCGAACGACTGCCGACACCGATACA[T/C]
GGGTACCGGGGCCGACAACCGCACAACGGGCACGGGCGACACCGAAAGGACGAGGACGGGGCAGCGAGGGAGAGGGATCCTTACCACCACGCGACGAGGC

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 45.60% 14.10% 40.27% 0.00% NA
All Indica  2759 21.20% 21.10% 57.70% 0.00% NA
All Japonica  1512 95.40% 1.60% 2.98% 0.00% NA
Aus  269 12.60% 17.50% 69.89% 0.00% NA
Indica I  595 17.50% 10.60% 71.93% 0.00% NA
Indica II  465 23.70% 10.50% 65.81% 0.00% NA
Indica III  913 19.90% 34.70% 45.35% 0.00% NA
Indica Intermediate  786 23.90% 19.60% 56.49% 0.00% NA
Temperate Japonica  767 93.70% 2.90% 3.39% 0.00% NA
Tropical Japonica  504 96.60% 0.40% 2.98% 0.00% NA
Japonica Intermediate  241 98.30% 0.00% 1.66% 0.00% NA
VI/Aromatic  96 35.40% 5.20% 59.38% 0.00% NA
Intermediate  90 68.90% 7.80% 23.33% 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
vg1207844031 A -> G LOC_Os12g13860.1 downstream_gene_variant ; 4190.0bp to feature; MODIFIER silent_mutation Average:17.251; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 N N N N
vg1207844031 A -> G LOC_Os12g13850-LOC_Os12g13860 intergenic_region ; MODIFIER silent_mutation Average:17.251; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207844031 NA 7.66E-06 mr1147 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
vg1207844031 5.59E-07 5.62E-07 mr1258 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
vg1207844031 1.14E-07 1.14E-07 mr1258 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
vg1207844031 4.87E-06 4.87E-06 mr1545 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
vg1207844031 4.49E-06 9.97E-06 mr1974 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
vg1207844031 9.25E-07 9.10E-06 mr1974 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