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Detailed information for vg1002106147:

Variant ID: vg1002106147 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2106147
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.59, T: 0.41, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCATTTATCTTGTATGTTTGCATTATGTCAATAATCATTTAATGAGTTAATTATTTGGAACGACATAACGGATTAGCTCATACTAGCCGCCAACCCGG[A/T]
CGTTGCACAAGCTATTACAAGAAATAAAAATATAAAAAAGACCAAATACATTTTATTGCTTAATAATCTAATTGGCATGAGTACAATGGATGTATGAAGA

Reverse complement sequence

TCTTCATACATCCATTGTACTCATGCCAATTAGATTATTAAGCAATAAAATGTATTTGGTCTTTTTTATATTTTTATTTCTTGTAATAGCTTGTGCAACG[T/A]
CCGGGTTGGCGGCTAGTATGAGCTAATCCGTTATGTCGTTCCAAATAATTAACTCATTAAATGATTATTGACATAATGCAAACATACAAGATAAATGGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.00% 25.40% 17.58% 16.00% NA
All Indica  2759 28.10% 15.50% 29.25% 27.11% NA
All Japonica  1512 60.70% 38.80% 0.26% 0.26% NA
Aus  269 38.70% 59.50% 1.49% 0.37% NA
Indica I  595 11.40% 26.90% 41.01% 20.67% NA
Indica II  465 28.80% 4.10% 32.47% 34.62% NA
Indica III  913 38.90% 14.00% 18.62% 28.48% NA
Indica Intermediate  786 27.70% 15.50% 30.79% 25.95% NA
Temperate Japonica  767 33.90% 65.60% 0.26% 0.26% NA
Tropical Japonica  504 92.90% 6.90% 0.20% 0.00% NA
Japonica Intermediate  241 78.80% 19.90% 0.41% 0.83% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 60.00% 18.90% 17.78% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1002106147 A -> T LOC_Os10g04460.1 upstream_gene_variant ; 4515.0bp to feature; MODIFIER silent_mutation Average:43.807; most accessible tissue: Minghui63 root, score: 56.226 N N N N
vg1002106147 A -> T LOC_Os10g04470.1 downstream_gene_variant ; 1609.0bp to feature; MODIFIER silent_mutation Average:43.807; most accessible tissue: Minghui63 root, score: 56.226 N N N N
vg1002106147 A -> T LOC_Os10g04460-LOC_Os10g04470 intergenic_region ; MODIFIER silent_mutation Average:43.807; most accessible tissue: Minghui63 root, score: 56.226 N N N N
vg1002106147 A -> DEL N N silent_mutation Average:43.807; most accessible tissue: Minghui63 root, score: 56.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002106147 NA 1.38E-13 Grain_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1002106147 8.39E-06 NA mr1486 Ind_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
vg1002106147 4.59E-07 NA mr1588 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
vg1002106147 5.00E-06 2.07E-06 mr1588 Ind_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
vg1002106147 NA 1.19E-06 mr1709 Ind_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
vg1002106147 NA 5.53E-09 mr1709_2 Ind_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