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Detailed information for vg1215077450:

Variant ID: vg1215077450 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15077450
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAATTTATTCCAGTGTTATTAGTACTGTACATCTATTACTGTACTAATGGCTCATTTTACCAGCAAAAGTTTTACAATATTGTTTTATTTAATCTTGCT[G/A]
CAAGAAAATAAATTTAGCATGTTGATTTTATAACTTTCTTTTATCTCTGTTGGAACCTGTTGTTCAAAAGTACAAAATTTGTGACCTTATTTCCAACTGT

Reverse complement sequence

ACAGTTGGAAATAAGGTCACAAATTTTGTACTTTTGAACAACAGGTTCCAACAGAGATAAAAGAAAGTTATAAAATCAACATGCTAAATTTATTTTCTTG[C/T]
AGCAAGATTAAATAAAACAATATTGTAAAACTTTTGCTGGTAAAATGAGCCATTAGTACAGTAATAGATGTACAGTACTAATAACACTGGAATAAATTTT

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% 0.30% 1.16% 6.52% NA
All Indica  2759 98.80% 0.00% 0.25% 0.98% NA
All Japonica  1512 79.20% 0.80% 2.98% 17.06% NA
Aus  269 96.30% 0.00% 0.74% 2.97% NA
Indica I  595 98.80% 0.00% 0.00% 1.18% NA
Indica II  465 97.00% 0.00% 0.65% 2.37% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 98.50% 0.00% 0.38% 1.15% NA
Temperate Japonica  767 91.70% 0.10% 0.39% 7.82% NA
Tropical Japonica  504 61.90% 2.20% 7.54% 28.37% NA
Japonica Intermediate  241 75.50% 0.00% 1.66% 22.82% NA
VI/Aromatic  96 86.50% 3.10% 0.00% 10.42% NA
Intermediate  90 93.30% 0.00% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1215077450 G -> DEL N N silent_mutation Average:9.775; most accessible tissue: Callus, score: 17.488 N N N N
vg1215077450 G -> A LOC_Os12g25959.1 upstream_gene_variant ; 3813.0bp to feature; MODIFIER silent_mutation Average:9.775; most accessible tissue: Callus, score: 17.488 N N N N
vg1215077450 G -> A LOC_Os12g25968.1 upstream_gene_variant ; 2474.0bp to feature; MODIFIER silent_mutation Average:9.775; most accessible tissue: Callus, score: 17.488 N N N N
vg1215077450 G -> A LOC_Os12g25980.1 intron_variant ; MODIFIER silent_mutation Average:9.775; most accessible tissue: Callus, score: 17.488 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215077450 NA 9.39E-06 mr1228_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
vg1215077450 NA 5.18E-07 mr1308_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
vg1215077450 1.01E-06 1.01E-06 mr1424_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
vg1215077450 NA 9.88E-06 mr1575_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
vg1215077450 NA 1.23E-06 mr1606_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
vg1215077450 NA 6.44E-06 mr1819_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
vg1215077450 4.57E-08 4.57E-08 mr1846_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
vg1215077450 NA 3.63E-06 mr1860_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
vg1215077450 NA 2.61E-06 mr1866_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
vg1215077450 NA 5.09E-06 mr1884_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
vg1215077450 5.84E-06 5.84E-06 mr1938_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