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Detailed information for vg1217937627:

Variant ID: vg1217937627 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17937627
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


ACGAATCTTTTGAGCCTAATTAGTCCATGATTAGCCATAAGTGCTACAGTAACCCATATGTGCTAATGATTGATTAATTAGGCTCAAAAGATTCATCCTG[C/T]
GGTTTCCAGGCGAGTTATGAAATTAGTTTTTTCATTCGTGTCCGAAAAACCCTTCAGACATCCGGTCAAACATCCAATGTGATAGCCAAAAAATTTCTTT

Reverse complement sequence

AAAGAAATTTTTTGGCTATCACATTGGATGTTTGACCGGATGTCTGAAGGGTTTTTCGGACACGAATGAAAAAACTAATTTCATAACTCGCCTGGAAACC[G/A]
CAGGATGAATCTTTTGAGCCTAATTAATCAATCATTAGCACATATGGGTTACTGTAGCACTTATGGCTAATCATGGACTAATTAGGCTCAAAAGATTCGT

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 92.80% 7.20% 0.00% 0.00% NA
All Indica  2759 96.60% 3.40% 0.00% 0.00% NA
All Japonica  1512 92.40% 7.60% 0.00% 0.00% NA
Aus  269 62.50% 37.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 90.10% 9.90% 0.00% 0.00% NA
Indica III  913 97.40% 2.60% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 79.80% 20.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg1217937627 C -> T LOC_Os12g30000.1 downstream_gene_variant ; 1550.0bp to feature; MODIFIER silent_mutation Average:53.16; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg1217937627 C -> T LOC_Os12g29990-LOC_Os12g30000 intergenic_region ; MODIFIER silent_mutation Average:53.16; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217937627 4.67E-06 1.57E-06 mr1289 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
vg1217937627 NA 2.94E-07 mr1364 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
vg1217937627 NA 6.32E-08 mr1403 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
vg1217937627 NA 2.43E-07 mr1443 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
vg1217937627 NA 4.62E-06 mr1884 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
vg1217937627 NA 1.39E-06 mr1498_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