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Detailed information for vg1206606922:

Variant ID: vg1206606922 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 6606922
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTGGCTATTATGTGAAGAAAAATTATATACTAAAGGCCGATGCTTGATTTCAAAAGTTTGGACGAAATTGGCAAAGTCATAGACCAGGGGTGGTCTGAC[C/T]
GGCATTGCACAGCGGTCTGACCGGTGGTACCTGCGGTCTGACCGGCTCTGCATGGCCGGTCTGACCGGGCAGACAGGGTGGTCTGACCGGCATTGCGTGG

Reverse complement sequence

CCACGCAATGCCGGTCAGACCACCCTGTCTGCCCGGTCAGACCGGCCATGCAGAGCCGGTCAGACCGCAGGTACCACCGGTCAGACCGCTGTGCAATGCC[G/A]
GTCAGACCACCCCTGGTCTATGACTTTGCCAATTTCGTCCAAACTTTTGAAATCAAGCATCGGCCTTTAGTATATAATTTTTCTTCACATAATAGCCAGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.90% 1.60% 26.45% 24.08% NA
All Indica  2759 21.30% 2.20% 38.53% 37.98% NA
All Japonica  1512 96.00% 0.30% 1.26% 2.45% NA
Aus  269 51.70% 1.90% 36.06% 10.41% NA
Indica I  595 46.40% 0.70% 40.17% 12.77% NA
Indica II  465 9.90% 1.90% 20.22% 67.96% NA
Indica III  913 9.20% 3.10% 49.07% 38.66% NA
Indica Intermediate  786 23.20% 2.40% 35.88% 38.55% NA
Temperate Japonica  767 94.70% 0.50% 1.30% 3.52% NA
Tropical Japonica  504 97.20% 0.00% 1.19% 1.59% NA
Japonica Intermediate  241 97.90% 0.00% 1.24% 0.83% NA
VI/Aromatic  96 24.00% 2.10% 63.54% 10.42% NA
Intermediate  90 68.90% 3.30% 11.11% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1206606922 C -> DEL N N silent_mutation Average:18.719; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg1206606922 C -> T LOC_Os12g12080.1 upstream_gene_variant ; 3892.0bp to feature; MODIFIER silent_mutation Average:18.719; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg1206606922 C -> T LOC_Os12g12080.2 upstream_gene_variant ; 3896.0bp to feature; MODIFIER silent_mutation Average:18.719; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg1206606922 C -> T LOC_Os12g12080.3 upstream_gene_variant ; 3896.0bp to feature; MODIFIER silent_mutation Average:18.719; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg1206606922 C -> T LOC_Os12g12080.4 upstream_gene_variant ; 3896.0bp to feature; MODIFIER silent_mutation Average:18.719; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg1206606922 C -> T LOC_Os12g12060.1 downstream_gene_variant ; 1643.0bp to feature; MODIFIER silent_mutation Average:18.719; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg1206606922 C -> T LOC_Os12g12040-LOC_Os12g12060 intergenic_region ; MODIFIER silent_mutation Average:18.719; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1206606922 7.68E-07 NA mr1383 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