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Detailed information for vg1217437473:

Variant ID: vg1217437473 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17437473
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


AAATACGATGATGGTTGTCTAGCAGTCTGAGGTCGTCCATAACAAAGGCTAACTAAACATGACTCAATTAGAACACCCAAGGGCTAAACTATATTTGGAC[C/T]
GAATGAGGTATGTTAGTTGTTTCGCAGATTTCGAGAAGCTCAGGTGGAATTTTGACGTGAGACTATAACCATCTAAAAGTAGAGTTAAAGACCTATCCAA

Reverse complement sequence

TTGGATAGGTCTTTAACTCTACTTTTAGATGGTTATAGTCTCACGTCAAAATTCCACCTGAGCTTCTCGAAATCTGCGAAACAACTAACATACCTCATTC[G/A]
GTCCAAATATAGTTTAGCCCTTGGGTGTTCTAATTGAGTCATGTTTAGTTAGCCTTTGTTATGGACGACCTCAGACTGCTAGACAACCATCATCGTATTT

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 93.80% 6.00% 0.15% 0.00% NA
All Indica  2759 93.80% 5.90% 0.25% 0.00% NA
All Japonica  1512 92.50% 7.50% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 82.40% 16.80% 0.86% 0.00% NA
Indica III  913 96.60% 3.30% 0.11% 0.00% NA
Indica Intermediate  786 93.30% 6.50% 0.25% 0.00% NA
Temperate Japonica  767 87.10% 12.90% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg1217437473 C -> T LOC_Os12g29370.1 upstream_gene_variant ; 4076.0bp to feature; MODIFIER silent_mutation Average:30.797; most accessible tissue: Callus, score: 53.711 N N N N
vg1217437473 C -> T LOC_Os12g29360.1 downstream_gene_variant ; 4127.0bp to feature; MODIFIER silent_mutation Average:30.797; most accessible tissue: Callus, score: 53.711 N N N N
vg1217437473 C -> T LOC_Os12g29360-LOC_Os12g29370 intergenic_region ; MODIFIER silent_mutation Average:30.797; most accessible tissue: Callus, score: 53.711 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217437473 NA 5.21E-06 mr1711_2 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
vg1217437473 3.34E-06 NA mr1991_2 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