Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1218622121:

Variant ID: vg1218622121 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18622121
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCAGTTTTGTGAGTATAATGAAGAAACTTATTTGTGAAAATCATTGAGGAAGCGATGATGATAAAGACAAATTATGTCTGTGTATGAGTGTGCATTTGC[G/A]
CGTGTTTGGGGGATTTCTATACCATATGTAGGTTTTGGATATGCATTTTCCGCCAGGAAAAATGGGGTATGCAGTGCATTTGAATTTACTACGGTTATAA

Reverse complement sequence

TTATAACCGTAGTAAATTCAAATGCACTGCATACCCCATTTTTCCTGGCGGAAAATGCATATCCAAAACCTACATATGGTATAGAAATCCCCCAAACACG[C/T]
GCAAATGCACACTCATACACAGACATAATTTGTCTTTATCATCATCGCTTCCTCAATGATTTTCACAAATAAGTTTCTTCATTATACTCACAAAACTGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.30% 0.50% 0.21% 0.00% NA
All Indica  2759 99.60% 0.30% 0.04% 0.00% NA
All Japonica  1512 98.30% 1.10% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 1.70% 0.65% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 97.90% 1.20% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1218622121 G -> A LOC_Os12g31000.1 downstream_gene_variant ; 974.0bp to feature; MODIFIER silent_mutation Average:39.689; most accessible tissue: Callus, score: 56.83 N N N N
vg1218622121 G -> A LOC_Os12g31000-LOC_Os12g31020 intergenic_region ; MODIFIER silent_mutation Average:39.689; most accessible tissue: Callus, score: 56.83 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218622121 4.63E-06 3.10E-08 mr1531_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