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Detailed information for vg1010296106:

Variant ID: vg1010296106 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10296106
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCATTCTCTAAATGTTTAATGCCGTTGACTTTTTTAAACGTGTTTGACCGTTCGTCTTATTCAAAAACTTTTGTGAAATATGTAAAACTATATGTATA[C/T]
ATAAAAGTATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATAATTACTTAAATTTTTTAAATAAGATGAATGGTCAAACTTTTTAAAAAAGTCA

Reverse complement sequence

TGACTTTTTTAAAAAGTTTGACCATTCATCTTATTTAAAAAATTTAAGTAATTATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATACTTTTAT[G/A]
TATACATATAGTTTTACATATTTCACAAAAGTTTTTGAATAAGACGAACGGTCAAACACGTTTAAAAAAGTCAACGGCATTAAACATTTAGAGAATGAGG

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 96.20% 3.80% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 89.20% 10.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 93.20% 6.80% 0.00% 0.00% NA
Tropical Japonica  504 80.20% 19.80% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg1010296106 C -> T LOC_Os10g20440.1 downstream_gene_variant ; 3988.0bp to feature; MODIFIER silent_mutation Average:40.6; most accessible tissue: Callus, score: 62.044 N N N N
vg1010296106 C -> T LOC_Os10g20450.1 downstream_gene_variant ; 193.0bp to feature; MODIFIER silent_mutation Average:40.6; most accessible tissue: Callus, score: 62.044 N N N N
vg1010296106 C -> T LOC_Os10g20460.1 downstream_gene_variant ; 968.0bp to feature; MODIFIER silent_mutation Average:40.6; most accessible tissue: Callus, score: 62.044 N N N N
vg1010296106 C -> T LOC_Os10g20450-LOC_Os10g20460 intergenic_region ; MODIFIER silent_mutation Average:40.6; most accessible tissue: Callus, score: 62.044 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010296106 NA 4.20E-06 mr1109_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
vg1010296106 NA 1.67E-06 mr1112_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
vg1010296106 1.68E-06 4.31E-08 mr1563_2 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