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Detailed information for vg1201039384:

Variant ID: vg1201039384 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 1039384
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGTCATTCCATATGATTTGGAAAGCTTCAGTTCCTTAGATCAAATGGCAAAATAGGAAAATTTTCTAGAATTTAAATCATATGAAATTCCTATGTAAAT[C/A]
CTTTAGGCCCCCTTTGATTCGTAGGAAAAGTGTAGGGAATTTGAAGGATTTCAATCCTATGGAAAAAATTCCTATGAAAGCTTTTGAAACAAAGGATTGA

Reverse complement sequence

TCAATCCTTTGTTTCAAAAGCTTTCATAGGAATTTTTTCCATAGGATTGAAATCCTTCAAATTCCCTACACTTTTCCTACGAATCAAAGGGGGCCTAAAG[G/T]
ATTTACATAGGAATTTCATATGATTTAAATTCTAGAAAATTTTCCTATTTTGCCATTTGATCTAAGGAACTGAAGCTTTCCAAATCATATGGAATGACTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.20% 3.00% 0.87% 0.00% NA
All Indica  2759 93.60% 4.90% 1.45% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 81.30% 13.30% 5.38% 0.00% NA
Indica II  465 95.70% 4.10% 0.22% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 94.40% 4.80% 0.76% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1201039384 C -> A LOC_Os12g02850.1 upstream_gene_variant ; 1837.0bp to feature; MODIFIER silent_mutation Average:23.424; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1201039384 C -> A LOC_Os12g02870.1 upstream_gene_variant ; 4149.0bp to feature; MODIFIER silent_mutation Average:23.424; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1201039384 C -> A LOC_Os12g02860.1 downstream_gene_variant ; 1579.0bp to feature; MODIFIER silent_mutation Average:23.424; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1201039384 C -> A LOC_Os12g02850-LOC_Os12g02860 intergenic_region ; MODIFIER silent_mutation Average:23.424; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1201039384 1.61E-06 NA mr1719 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