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Detailed information for vg0905608725:

Variant ID: vg0905608725 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5608725
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTCTTTCCCTTATGATGGCCTCGAATGACGATGGTTCCTGTGCTCCTCGTCGTTGATGGCGCCCCCGCACGTATCCTCACCCACAGCTCCCCGGTCGC[A/C]
CTCGCCTCGAGCTCTTGCCGCTACCGCCGTCCCGAGCTCCCGCGGCCGGTGGCTTCTCCCCTTCCACCACCATGCAGGACCCCTCTCCCTTCTCTCCCTC

Reverse complement sequence

GAGGGAGAGAAGGGAGAGGGGTCCTGCATGGTGGTGGAAGGGGAGAAGCCACCGGCCGCGGGAGCTCGGGACGGCGGTAGCGGCAAGAGCTCGAGGCGAG[T/G]
GCGACCGGGGAGCTGTGGGTGAGGATACGTGCGGGGGCGCCATCAACGACGAGGAGCACAGGAACCATCGTCATTCGAGGCCATCATAAGGGAAAGAGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.80% 10.20% 0.00% 0.00% NA
All Indica  2759 95.90% 4.10% 0.00% 0.00% NA
All Japonica  1512 81.50% 18.50% 0.00% 0.00% NA
Aus  269 89.60% 10.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 87.30% 12.70% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 94.50% 5.50% 0.00% 0.00% NA
Temperate Japonica  767 90.90% 9.10% 0.00% 0.00% NA
Tropical Japonica  504 82.30% 17.70% 0.00% 0.00% NA
Japonica Intermediate  241 49.80% 50.20% 0.00% 0.00% NA
VI/Aromatic  96 45.80% 54.20% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0905608725 A -> C LOC_Os09g10290.1 upstream_gene_variant ; 892.0bp to feature; MODIFIER silent_mutation Average:69.441; most accessible tissue: Zhenshan97 young leaf, score: 87.859 N N N N
vg0905608725 A -> C LOC_Os09g10300.1 upstream_gene_variant ; 1652.0bp to feature; MODIFIER silent_mutation Average:69.441; most accessible tissue: Zhenshan97 young leaf, score: 87.859 N N N N
vg0905608725 A -> C LOC_Os09g10290-LOC_Os09g10300 intergenic_region ; MODIFIER silent_mutation Average:69.441; most accessible tissue: Zhenshan97 young leaf, score: 87.859 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905608725 NA 4.74E-06 mr1064 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
vg0905608725 1.28E-06 1.61E-07 mr1826_2 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