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Detailed information for vg0901284560:

Variant ID: vg0901284560 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 1284560
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAAATTGAAGTGCATTCCGATTAAGTATGTATGTGTGTATATATTGGGGGCTCTGAATATATATAGTTGCGGACTAATCGAGCGAGGACTAGAGGCAAG[G/A]
TGAATGTCACTTGGCAAAATTCAACTAAATAAAACCCGATTGTTCTACAGGGTATACATAGACATTTATAGAGGAAAATAGAGGTAGGGTTAAGTGCTAA

Reverse complement sequence

TTAGCACTTAACCCTACCTCTATTTTCCTCTATAAATGTCTATGTATACCCTGTAGAACAATCGGGTTTTATTTAGTTGAATTTTGCCAAGTGACATTCA[C/T]
CTTGCCTCTAGTCCTCGCTCGATTAGTCCGCAACTATATATATTCAGAGCCCCCAATATATACACACATACATACTTAATCGGAATGCACTTCAATTTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.60% 3.20% 0.19% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.60% 9.90% 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 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.30% 2.30% 0.39% 0.00% NA
Tropical Japonica  504 80.60% 18.80% 0.60% 0.00% NA
Japonica Intermediate  241 83.80% 14.90% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0901284560 G -> A LOC_Os09g02790.1 upstream_gene_variant ; 1581.0bp to feature; MODIFIER silent_mutation Average:43.826; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N
vg0901284560 G -> A LOC_Os09g02800.1 downstream_gene_variant ; 1070.0bp to feature; MODIFIER silent_mutation Average:43.826; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N
vg0901284560 G -> A LOC_Os09g02805.1 downstream_gene_variant ; 3598.0bp to feature; MODIFIER silent_mutation Average:43.826; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N
vg0901284560 G -> A LOC_Os09g02790-LOC_Os09g02800 intergenic_region ; MODIFIER silent_mutation Average:43.826; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0901284560 2.08E-06 NA Grain_thickness 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
vg0901284560 2.94E-07 NA Grain_width Jap_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