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Detailed information for vg1002106037:

Variant ID: vg1002106037 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2106037
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCAAGATTTGATTTTTCTTTTCCCATTCTCATATCAAGGTGGGGAAGGCAGGTGACAAAAAATACATCAACTGTAGAGGTGGCAATTTCCAAGGTGTG[A/G]
GTATCAACTCTCCATTTATCTTGTATGTTTGCATTATGTCAATAATCATTTAATGAGTTAATTATTTGGAACGACATAACGGATTAGCTCATACTAGCCG

Reverse complement sequence

CGGCTAGTATGAGCTAATCCGTTATGTCGTTCCAAATAATTAACTCATTAAATGATTATTGACATAATGCAAACATACAAGATAAATGGAGAGTTGATAC[T/C]
CACACCTTGGAAATTGCCACCTCTACAGTTGATGTATTTTTTGTCACCTGCCTTCCCCACCTTGATATGAGAATGGGAAAAGAAAAATCAAATCTTGAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.20% 12.70% 0.06% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 63.40% 36.50% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 2.50% 0.00% 0.00% NA
Temperate Japonica  767 34.40% 65.30% 0.26% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 80.90% 19.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 8.90% 1.11% 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
vg1002106037 A -> G LOC_Os10g04460.1 upstream_gene_variant ; 4405.0bp to feature; MODIFIER silent_mutation Average:50.339; most accessible tissue: Callus, score: 82.386 N N N N
vg1002106037 A -> G LOC_Os10g04470.1 downstream_gene_variant ; 1719.0bp to feature; MODIFIER silent_mutation Average:50.339; most accessible tissue: Callus, score: 82.386 N N N N
vg1002106037 A -> G LOC_Os10g04460-LOC_Os10g04470 intergenic_region ; MODIFIER silent_mutation Average:50.339; most accessible tissue: Callus, score: 82.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002106037 6.24E-06 NA Grain_weight 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
vg1002106037 3.97E-06 3.12E-07 Grain_weight Ind_All YES 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
vg1002106037 NA 3.25E-06 mr1179 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