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Detailed information for vg1206852097:

Variant ID: vg1206852097 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 6852097
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTGAGGCAAAACCTAGAAGAAACCCTTCATCACACCGACTTTCAAATTTGGTTAGTCTAACACCCTTTCGGTGAATATAACACTTGCAACCAAAAACTC[A/G]
AAAATAGGCAACATTTGGCTTCCTCCCAACAATTAGCTCATAGGAAGTCTTTTTCAAGAGACGATGCAAATAAAGCCTATTGGTTGCATGGCAAGCGGTG

Reverse complement sequence

CACCGCTTGCCATGCAACCAATAGGCTTTATTTGCATCGTCTCTTGAAAAAGACTTCCTATGAGCTAATTGTTGGGAGGAAGCCAAATGTTGCCTATTTT[T/C]
GAGTTTTTGGTTGCAAGTGTTATATTCACCGAAAGGGTGTTAGACTAACCAAATTTGAAAGTCGGTGTGATGAAGGGTTTCTTCTAGGTTTTGCCTCAAA

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 77.70% 0.80% 0.30% 21.22% NA
All Indica  2759 98.90% 0.10% 0.25% 0.80% NA
All Japonica  1512 39.40% 0.30% 0.40% 59.99% NA
Aus  269 85.90% 1.10% 0.37% 12.64% NA
Indica I  595 99.20% 0.00% 0.17% 0.67% NA
Indica II  465 98.30% 0.00% 0.00% 1.72% NA
Indica III  913 99.20% 0.10% 0.44% 0.22% NA
Indica Intermediate  786 98.60% 0.10% 0.25% 1.02% NA
Temperate Japonica  767 44.10% 0.30% 0.39% 55.28% NA
Tropical Japonica  504 25.20% 0.00% 0.40% 74.40% NA
Japonica Intermediate  241 53.90% 0.80% 0.41% 44.81% NA
VI/Aromatic  96 56.20% 22.90% 0.00% 20.83% NA
Intermediate  90 72.20% 5.60% 0.00% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1206852097 A -> DEL N N silent_mutation Average:10.456; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N
vg1206852097 A -> G LOC_Os12g12440.1 upstream_gene_variant ; 3765.0bp to feature; MODIFIER silent_mutation Average:10.456; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N
vg1206852097 A -> G LOC_Os12g12450.1 intron_variant ; MODIFIER silent_mutation Average:10.456; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1206852097 NA 4.00E-06 mr1460 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
vg1206852097 4.27E-06 NA mr1576 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
vg1206852097 7.57E-06 NA mr1824 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