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Detailed information for vg1207774257:

Variant ID: vg1207774257 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7774257
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGTATTTGTGATGTATATGGCATTGGATTGTTCCAATTTGTATTGTTGGACAATGTTTTTGACAAGATAAATTCCTCAGTAAACTAATAAGCATTAGAA[G/A]
TATTCTCTAGATAACTCTTCTTTCACCCATATGTTTTATTTTCTTTATATGTCCATGTTCATTTATTCTGATCAGTGTCCGTGGCTTTACCGCGGGGCAC

Reverse complement sequence

GTGCCCCGCGGTAAAGCCACGGACACTGATCAGAATAAATGAACATGGACATATAAAGAAAATAAAACATATGGGTGAAAGAAGAGTTATCTAGAGAATA[C/T]
TTCTAATGCTTATTAGTTTACTGAGGAATTTATCTTGTCAAAAACATTGTCCAACAATACAAATTGGAACAATCCAATGCCATATACATCACAAATACAT

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 92.00% 7.90% 0.08% 0.00% NA
All Indica  2759 86.70% 13.30% 0.07% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 97.80% 1.50% 0.74% 0.00% NA
Indica I  595 88.70% 11.30% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 83.10% 16.90% 0.00% 0.00% NA
Indica Intermediate  786 82.40% 17.30% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 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 96.70% 3.30% 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
vg1207774257 G -> A LOC_Os12g13770.1 downstream_gene_variant ; 2862.0bp to feature; MODIFIER silent_mutation Average:56.795; most accessible tissue: Callus, score: 80.491 N N N N
vg1207774257 G -> A LOC_Os12g13760-LOC_Os12g13770 intergenic_region ; MODIFIER silent_mutation Average:56.795; most accessible tissue: Callus, score: 80.491 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207774257 NA 3.71E-07 mr1066 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
vg1207774257 8.33E-07 4.34E-07 mr1196 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
vg1207774257 8.20E-06 8.17E-06 mr1497 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
vg1207774257 5.77E-06 NA mr1637 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
vg1207774257 NA 4.99E-06 mr1817 Ind_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
vg1207774257 NA 4.53E-06 mr1888 Ind_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