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Detailed information for vg0906899491:

Variant ID: vg0906899491 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6899491
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TAATTTGTTGGGTCAATGGCAGATGGTCTATAATGTTTTGCGTATAGATTCTTTTGTATTTGTTATCCGTTATTAGCTTTGCCCAGGCTCAAGAAAATTT[A/G]
TAGATAGACCACTGCTAGGAGTGATGACATATAGTGGGAAAATTGTTCGAAGAGGAAACAAACTGACAACCATTTTAAGTTAATCATCATTACGGTGAAC

Reverse complement sequence

GTTCACCGTAATGATGATTAACTTAAAATGGTTGTCAGTTTGTTTCCTCTTCGAACAATTTTCCCACTATATGTCATCACTCCTAGCAGTGGTCTATCTA[T/C]
AAATTTTCTTGAGCCTGGGCAAAGCTAATAACGGATAACAAATACAAAAGAATCTATACGCAAAACATTATAGACCATCTGCCATTGACCCAACAAATTA

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 93.80% 6.10% 0.02% 0.02% NA
All Indica  2759 93.00% 7.00% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.30% 0.07% 0.07% NA
Aus  269 67.30% 32.70% 0.00% 0.00% NA
Indica I  595 82.50% 17.50% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 91.20% 8.80% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.40% 0.20% 0.20% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg0906899491 A -> G LOC_Os09g12200.1 downstream_gene_variant ; 1335.0bp to feature; MODIFIER silent_mutation Average:50.161; most accessible tissue: Callus, score: 71.788 N N N N
vg0906899491 A -> G LOC_Os09g12200-LOC_Os09g12210 intergenic_region ; MODIFIER silent_mutation Average:50.161; most accessible tissue: Callus, score: 71.788 N N N N
vg0906899491 A -> DEL N N silent_mutation Average:50.161; most accessible tissue: Callus, score: 71.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906899491 NA 7.55E-06 mr1331 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
vg0906899491 5.13E-06 5.12E-06 mr1421 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