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Detailed information for vg0909417437:

Variant ID: vg0909417437 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9417437
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTTCGCCTTATAACTCCATCTCCAGCGCCTCTTATGCCATTAGATCTCCATCTCCGACGATGTTTTCCTCATAGCTCCTGCATTCCAATTTCCATTTC[A/G]
GCATCCAATTGGAAGGTATTATCTCTAATGGTTCTAGCCTTTGAACAAAACAAATCAGCTATAAACTAGATTTCATCTTGAGCATTGTGTTCCTCCTTTT

Reverse complement sequence

AAAAGGAGGAACACAATGCTCAAGATGAAATCTAGTTTATAGCTGATTTGTTTTGTTCAAAGGCTAGAACCATTAGAGATAATACCTTCCAATTGGATGC[T/C]
GAAATGGAAATTGGAATGCAGGAGCTATGAGGAAAACATCGTCGGAGATGGAGATCTAATGGCATAAGAGGCGCTGGAGATGGAGTTATAAGGCGAAGAG

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 97.00% 3.00% 0.02% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 94.60% 5.40% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 87.50% 12.50% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 49.00% 51.00% 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
vg0909417437 A -> G LOC_Os09g15389.1 downstream_gene_variant ; 2667.0bp to feature; MODIFIER silent_mutation Average:34.549; most accessible tissue: Callus, score: 78.364 N N N N
vg0909417437 A -> G LOC_Os09g15389.2 downstream_gene_variant ; 4377.0bp to feature; MODIFIER silent_mutation Average:34.549; most accessible tissue: Callus, score: 78.364 N N N N
vg0909417437 A -> G LOC_Os09g15380-LOC_Os09g15389 intergenic_region ; MODIFIER silent_mutation Average:34.549; most accessible tissue: Callus, score: 78.364 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909417437 NA 6.04E-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
vg0909417437 NA 1.14E-06 mr1206 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
vg0909417437 NA 5.69E-07 mr1951 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
vg0909417437 2.29E-06 2.30E-06 mr1994 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