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Detailed information for vg1215101661:

Variant ID: vg1215101661 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15101661
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACCTTATTTCAGTTTTAGCTTCCGCATAAAGTTTTAAATTAGCCTATTCACCCCCCCTCTAGCCCTAATTGACCCTTTCAGGGCCCCTCCCCCCGCTGC[C/A]
CCGTCCTCGTCCTTTCGGAGTCGCCCCGTGCCTGTTGTGCGGTTGTCAATCCCGGTACCCGTGTACCGGTGTCGATAGTTGTTCGTGTGTGCATGTGGTG

Reverse complement sequence

CACCACATGCACACACGAACAACTATCGACACCGGTACACGGGTACCGGGATTGACAACCGCACAACAGGCACGGGGCGACTCCGAAAGGACGAGGACGG[G/T]
GCAGCGGGGGGAGGGGCCCTGAAAGGGTCAATTAGGGCTAGAGGGGGGGTGAATAGGCTAATTTAAAACTTTATGCGGAAGCTAAAACTGAAATAAGGTT

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 98.90% 0.80% 0.36% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 96.80% 2.30% 0.93% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 94.50% 3.90% 1.56% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 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
vg1215101661 C -> A LOC_Os12g26000.1 upstream_gene_variant ; 2659.0bp to feature; MODIFIER silent_mutation Average:56.38; most accessible tissue: Zhenshan97 root, score: 74.877 N N N N
vg1215101661 C -> A LOC_Os12g26000-LOC_Os12g26010 intergenic_region ; MODIFIER silent_mutation Average:56.38; most accessible tissue: Zhenshan97 root, score: 74.877 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215101661 1.00E-06 1.00E-06 mr1067_2 Jap_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
vg1215101661 NA 8.48E-07 mr1457_2 Jap_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
vg1215101661 NA 4.90E-07 mr1458_2 Jap_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
vg1215101661 4.13E-06 NA mr1613_2 Jap_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
vg1215101661 3.14E-06 3.28E-08 mr1718_2 Jap_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