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Detailed information for vg1003720429:

Variant ID: vg1003720429 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3720429
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAGATCTAATTTGTGTAATAAATTTTTTAAGCCTAATTAATCTATAATTAGCACATATTTACTGTAGCATCACATAGGCTAATCATGGATTAATTAGGT[A/T]
CAATAGATTTATCTCGTGAGTTAGGCTAAGATTATAGAATTGGTTTTATCAATAATCTATGTTTAATACTTCTAATTATTACCAAATATCCGATCTGATA

Reverse complement sequence

TATCAGATCGGATATTTGGTAATAATTAGAAGTATTAAACATAGATTATTGATAAAACCAATTCTATAATCTTAGCCTAACTCACGAGATAAATCTATTG[T/A]
ACCTAATTAATCCATGATTAGCCTATGTGATGCTACAGTAAATATGTGCTAATTATAGATTAATTAGGCTTAAAAAATTTATTACACAAATTAGATCTTA

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 29.50% 11.30% 0.80% 58.36% NA
All Indica  2759 12.10% 5.30% 0.51% 82.06% NA
All Japonica  1512 59.60% 19.30% 1.32% 19.78% NA
Aus  269 35.70% 4.50% 1.12% 58.74% NA
Indica I  595 4.00% 0.00% 0.50% 95.46% NA
Indica II  465 32.00% 0.60% 0.43% 66.88% NA
Indica III  913 8.70% 11.80% 0.44% 79.08% NA
Indica Intermediate  786 10.60% 4.50% 0.64% 84.35% NA
Temperate Japonica  767 88.00% 11.00% 0.39% 0.65% NA
Tropical Japonica  504 24.80% 20.20% 0.79% 54.17% NA
Japonica Intermediate  241 41.90% 44.00% 5.39% 8.71% NA
VI/Aromatic  96 31.20% 68.80% 0.00% 0.00% NA
Intermediate  90 37.80% 20.00% 1.11% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003720429 A -> T LOC_Os10g07060.1 downstream_gene_variant ; 3180.0bp to feature; MODIFIER silent_mutation Average:12.192; most accessible tissue: Callus, score: 84.576 N N N N
vg1003720429 A -> T LOC_Os10g07060-LOC_Os10g07080 intergenic_region ; MODIFIER silent_mutation Average:12.192; most accessible tissue: Callus, score: 84.576 N N N N
vg1003720429 A -> DEL N N silent_mutation Average:12.192; most accessible tissue: Callus, score: 84.576 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003720429 2.22E-07 NA Grain_weight 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
vg1003720429 NA 5.36E-06 Grain_weight Jap_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