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Detailed information for vg0907972595:

Variant ID: vg0907972595 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7972595
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GTGGATTTTGGCCAACCGAGCAAAGATGGTTTCTCCACCAGTGGATACTTTTGGCTCAGTTGGAGAGATAAATTCTTAAGCAAGACGAGAATGCATCAAA[G/C]
ACCACATGCTTCAAACATGGCATTAGAGTAAAAATTGAGAAATTATACAACTCTAAATTTGCCATCACCTAAGTACATCACTAGCATACATCATATTCCA

Reverse complement sequence

TGGAATATGATGTATGCTAGTGATGTACTTAGGTGATGGCAAATTTAGAGTTGTATAATTTCTCAATTTTTACTCTAATGCCATGTTTGAAGCATGTGGT[C/G]
TTTGATGCATTCTCGTCTTGCTTAAGAATTTATCTCTCCAACTGAGCCAAAAGTATCCACTGGTGGAGAAACCATCTTTGCTCGGTTGGCCAAAATCCAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.20% 11.60% 0.28% 0.00% NA
All Indica  2759 92.40% 7.60% 0.00% 0.00% NA
All Japonica  1512 77.80% 21.30% 0.86% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 82.80% 17.20% 0.00% 0.00% NA
Indica Intermediate  786 95.30% 4.70% 0.00% 0.00% NA
Temperate Japonica  767 75.20% 23.10% 1.69% 0.00% NA
Tropical Japonica  504 83.30% 16.70% 0.00% 0.00% NA
Japonica Intermediate  241 74.70% 25.30% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0907972595 G -> C LOC_Os09g13650.1 downstream_gene_variant ; 4676.0bp to feature; MODIFIER silent_mutation Average:23.808; most accessible tissue: Minghui63 root, score: 31.271 N N N N
vg0907972595 G -> C LOC_Os09g13650.2 downstream_gene_variant ; 4676.0bp to feature; MODIFIER silent_mutation Average:23.808; most accessible tissue: Minghui63 root, score: 31.271 N N N N
vg0907972595 G -> C LOC_Os09g13650.3 downstream_gene_variant ; 4676.0bp to feature; MODIFIER silent_mutation Average:23.808; most accessible tissue: Minghui63 root, score: 31.271 N N N N
vg0907972595 G -> C LOC_Os09g13650-LOC_Os09g13660 intergenic_region ; MODIFIER silent_mutation Average:23.808; most accessible tissue: Minghui63 root, score: 31.271 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907972595 NA 2.39E-07 mr1057_2 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
vg0907972595 NA 1.20E-07 mr1548_2 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
vg0907972595 2.20E-06 2.20E-06 mr1548_2 Jap_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