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Detailed information for vg1223859563:

Variant ID: vg1223859563 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23859563
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GCAGCCGGATCCACCGCCGCATCGCCTCTCGCCCACAGTCACCCGTCGATACCGCACCACTATCGCGCCCGTCCACGCACCTCAACGCCATCAGATCCGC[C/T]
GCTCCTCCTTGATGCTGGTCCTCCTCATCCCCAAACTGCCACCGGTCCTCCTCGTCGCCAAGCCATCACCGGAACTGCCTCGCCGCCACTCCTCATCCCC

Reverse complement sequence

GGGGATGAGGAGTGGCGGCGAGGCAGTTCCGGTGATGGCTTGGCGACGAGGAGGACCGGTGGCAGTTTGGGGATGAGGAGGACCAGCATCAAGGAGGAGC[G/A]
GCGGATCTGATGGCGTTGAGGTGCGTGGACGGGCGCGATAGTGGTGCGGTATCGACGGGTGACTGTGGGCGAGAGGCGATGCGGCGGTGGATCCGGCTGC

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 91.00% 8.90% 0.08% 0.00% NA
All Indica  2759 97.70% 2.30% 0.04% 0.00% NA
All Japonica  1512 77.20% 22.80% 0.07% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 90.80% 9.00% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 2.50% 0.00% 0.00% NA
Temperate Japonica  767 85.50% 14.30% 0.13% 0.00% NA
Tropical Japonica  504 73.60% 26.40% 0.00% 0.00% NA
Japonica Intermediate  241 58.10% 41.90% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 87.80% 10.00% 2.22% 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
vg1223859563 C -> T LOC_Os12g38820.1 upstream_gene_variant ; 79.0bp to feature; MODIFIER silent_mutation Average:70.276; most accessible tissue: Minghui63 flag leaf, score: 81.052 N N N N
vg1223859563 C -> T LOC_Os12g38830.1 upstream_gene_variant ; 1086.0bp to feature; MODIFIER silent_mutation Average:70.276; most accessible tissue: Minghui63 flag leaf, score: 81.052 N N N N
vg1223859563 C -> T LOC_Os12g38840.1 downstream_gene_variant ; 4025.0bp to feature; MODIFIER silent_mutation Average:70.276; most accessible tissue: Minghui63 flag leaf, score: 81.052 N N N N
vg1223859563 C -> T LOC_Os12g38820-LOC_Os12g38830 intergenic_region ; MODIFIER silent_mutation Average:70.276; most accessible tissue: Minghui63 flag leaf, score: 81.052 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223859563 4.50E-06 NA mr1907 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
vg1223859563 9.94E-06 NA mr1019_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
vg1223859563 NA 9.94E-07 mr1691_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
vg1223859563 NA 5.89E-06 mr1861_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