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Detailed information for vg0122207812:

Variant ID: vg0122207812 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 22207812
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, A: 0.15, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GCTCATGTACGGTGGGACACGGGCTCACGGATGGAGTCTTGGACCTCGGGGACGGCGGGGAACAACGGTGCTGGTTGTGCTTAATTGGAGAAGCTCAAGG[A/C]
GGCGGCGCCGGTGAGGAGCTCACGGGCGGCAGCGACGGGCTCGCGAACGACGGCGAGGAGCTCGAGGACGGCGCCGGGATCGGGGGAGGTGTTCGATGCG

Reverse complement sequence

CGCATCGAACACCTCCCCCGATCCCGGCGCCGTCCTCGAGCTCCTCGCCGTCGTTCGCGAGCCCGTCGCTGCCGCCCGTGAGCTCCTCACCGGCGCCGCC[T/G]
CCTTGAGCTTCTCCAATTAAGCACAACCAGCACCGTTGTTCCCCGCCGTCCCCGAGGTCCAAGACTCCATCCGTGAGCCCGTGTCCCACCGTACATGAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.80% 44.30% 0.15% 0.72% NA
All Indica  2759 86.80% 13.10% 0.07% 0.00% NA
All Japonica  1512 0.40% 97.30% 0.07% 2.25% NA
Aus  269 55.00% 44.60% 0.37% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 78.20% 21.80% 0.00% 0.00% NA
Indica Intermediate  786 83.10% 16.80% 0.13% 0.00% NA
Temperate Japonica  767 0.30% 96.60% 0.13% 3.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 94.60% 0.00% 4.56% NA
VI/Aromatic  96 9.40% 89.60% 1.04% 0.00% NA
Intermediate  90 35.60% 62.20% 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
vg0122207812 A -> DEL N N silent_mutation Average:73.831; most accessible tissue: Minghui63 flag leaf, score: 82.75 N N N N
vg0122207812 A -> C LOC_Os01g39420.1 downstream_gene_variant ; 3007.0bp to feature; MODIFIER silent_mutation Average:73.831; most accessible tissue: Minghui63 flag leaf, score: 82.75 N N N N
vg0122207812 A -> C LOC_Os01g39399.1 intron_variant ; MODIFIER silent_mutation Average:73.831; most accessible tissue: Minghui63 flag leaf, score: 82.75 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0122207812 NA 1.50E-21 mr1003 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
vg0122207812 NA 1.06E-21 mr1051 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
vg0122207812 2.52E-06 2.52E-06 mr1065 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
vg0122207812 2.16E-06 2.50E-06 mr1078 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
vg0122207812 NA 3.57E-06 mr1201 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
vg0122207812 NA 1.20E-06 mr1274 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
vg0122207812 NA 1.17E-11 mr1281 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
vg0122207812 NA 1.56E-08 mr1342 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
vg0122207812 7.66E-06 3.80E-06 mr1962 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
vg0122207812 NA 2.58E-25 mr1051_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
vg0122207812 NA 1.64E-22 mr1609_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