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Detailed information for vg1224819675:

Variant ID: vg1224819675 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24819675
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAGTCCACACAGTACATCCTACTAATACCATTGCTTATCATCCTTTCAGTTATCACAAAACCTGAAGAAAAGATACTCGCAATGCCTTGAGCAAAAAT[C/T]
TCCTTTCATTGCTTATTTTGTTAACTTTGTTGGATGATAAATGCACTGATTTTCTTGTTTTGGTTAGCAGGATGAATGCCATGTCTAGTTATCAATGACT

Reverse complement sequence

AGTCATTGATAACTAGACATGGCATTCATCCTGCTAACCAAAACAAGAAAATCAGTGCATTTATCATCCAACAAAGTTAACAAAATAAGCAATGAAAGGA[G/A]
ATTTTTGCTCAAGGCATTGCGAGTATCTTTTCTTCAGGTTTTGTGATAACTGAAAGGATGATAAGCAATGGTATTAGTAGGATGTACTGTGTGGACTTCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.80% 10.10% 0.00% 0.11% NA
All Indica  2759 93.10% 6.70% 0.00% 0.18% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 77.80% 22.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 97.60% 2.20% 0.00% 0.22% NA
Indica Intermediate  786 95.40% 4.20% 0.00% 0.38% 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 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg1224819675 C -> DEL N N silent_mutation Average:53.901; most accessible tissue: Zhenshan97 young leaf, score: 78.347 N N N N
vg1224819675 C -> T LOC_Os12g40130.1 upstream_gene_variant ; 1429.0bp to feature; MODIFIER silent_mutation Average:53.901; most accessible tissue: Zhenshan97 young leaf, score: 78.347 N N N N
vg1224819675 C -> T LOC_Os12g40140.1 upstream_gene_variant ; 3595.0bp to feature; MODIFIER silent_mutation Average:53.901; most accessible tissue: Zhenshan97 young leaf, score: 78.347 N N N N
vg1224819675 C -> T LOC_Os12g40115.1 downstream_gene_variant ; 2298.0bp to feature; MODIFIER silent_mutation Average:53.901; most accessible tissue: Zhenshan97 young leaf, score: 78.347 N N N N
vg1224819675 C -> T LOC_Os12g40120.1 intron_variant ; MODIFIER silent_mutation Average:53.901; most accessible tissue: Zhenshan97 young leaf, score: 78.347 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1224819675 NA 3.29E-06 mr1126 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
vg1224819675 NA 8.66E-10 mr1730 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
vg1224819675 NA 5.21E-06 mr1344_2 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
vg1224819675 NA 2.84E-16 mr1587_2 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
vg1224819675 NA 9.45E-09 mr1829_2 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