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Detailed information for vg1223900974:

Variant ID: vg1223900974 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23900974
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GGCCCGTTTAGTTCGTGAAAAGGAATTTTTTTAGATGTCACATCGGACGTTTGACCGGATATCGGAAAGGGTTTTCGGACACGAATGAAAAAACTAATTT[T/C]
ATAACTTGCTTGGAAACCGCGAGACGAATCTTTTGAGCCTAATTAATCTGTCATTAGCACATGTGGATTACTGTAGCACTTATGGCTAATCATGGACTAA

Reverse complement sequence

TTAGTCCATGATTAGCCATAAGTGCTACAGTAATCCACATGTGCTAATGACAGATTAATTAGGCTCAAAAGATTCGTCTCGCGGTTTCCAAGCAAGTTAT[A/G]
AAATTAGTTTTTTCATTCGTGTCCGAAAACCCTTTCCGATATCCGGTCAAACGTCCGATGTGACATCTAAAAAAATTCCTTTTCACGAACTAAACGGGCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.20% 12.80% 0.00% 0.00% NA
All Indica  2759 85.30% 14.70% 0.00% 0.00% NA
All Japonica  1512 87.80% 12.20% 0.00% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 71.60% 28.40% 0.00% 0.00% NA
Indica II  465 78.70% 21.30% 0.00% 0.00% NA
Indica III  913 96.50% 3.50% 0.00% 0.00% NA
Indica Intermediate  786 86.60% 13.40% 0.00% 0.00% NA
Temperate Japonica  767 89.40% 10.60% 0.00% 0.00% NA
Tropical Japonica  504 95.20% 4.80% 0.00% 0.00% NA
Japonica Intermediate  241 67.20% 32.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1223900974 T -> C LOC_Os12g38870.1 upstream_gene_variant ; 2670.0bp to feature; MODIFIER silent_mutation Average:46.195; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg1223900974 T -> C LOC_Os12g38870.2 upstream_gene_variant ; 2670.0bp to feature; MODIFIER silent_mutation Average:46.195; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg1223900974 T -> C LOC_Os12g38870-LOC_Os12g38880 intergenic_region ; MODIFIER silent_mutation Average:46.195; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223900974 8.23E-06 8.23E-06 mr1038 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
vg1223900974 NA 8.26E-06 mr1691 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
vg1223900974 NA 4.94E-08 mr1693 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
vg1223900974 NA 2.27E-08 mr1745 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