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Detailed information for vg1015794218:

Variant ID: vg1015794218 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15794218
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


TACATACATAGACCAAAAGAGGTCCCTCCGGCCCAGAGAAACAACCAATTTTTAGACAGCAGGGACAACACATGACCCATAAGTGAAGATACACCAGACA[C/T]
AGCGATTTAAAAAGCTTTCCAAAACACCTCCACAAAGTAACAGACGGCAAAAAAACTCTAACTAACACACCCCAGTTCTGATATTTCACAGTCCAGCACA

Reverse complement sequence

TGTGCTGGACTGTGAAATATCAGAACTGGGGTGTGTTAGTTAGAGTTTTTTTGCCGTCTGTTACTTTGTGGAGGTGTTTTGGAAAGCTTTTTAAATCGCT[G/A]
TGTCTGGTGTATCTTCACTTATGGGTCATGTGTTGTCCCTGCTGTCTAAAAATTGGTTGTTTCTCTGGGCCGGAGGGACCTCTTTTGGTCTATGTATGTA

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 99.00% 0.80% 0.19% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 97.10% 2.30% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.30% 4.60% 1.17% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1015794218 C -> T LOC_Os10g30380.1 upstream_gene_variant ; 1751.0bp to feature; MODIFIER silent_mutation Average:45.081; most accessible tissue: Callus, score: 65.498 N N N N
vg1015794218 C -> T LOC_Os10g30390.1 downstream_gene_variant ; 1960.0bp to feature; MODIFIER silent_mutation Average:45.081; most accessible tissue: Callus, score: 65.498 N N N N
vg1015794218 C -> T LOC_Os10g30380-LOC_Os10g30390 intergenic_region ; MODIFIER silent_mutation Average:45.081; most accessible tissue: Callus, score: 65.498 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015794218 5.83E-07 1.82E-08 mr1210 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
vg1015794218 NA 1.38E-07 mr1305 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
vg1015794218 5.86E-08 2.79E-10 mr1585 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
vg1015794218 1.94E-08 5.19E-10 mr1586 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
vg1015794218 NA 5.21E-06 mr1765 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
vg1015794218 NA 2.07E-06 mr1585_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