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Detailed information for vg0808948492:

Variant ID: vg0808948492 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8948492
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.70, A: 0.29, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


AATTAATGAGATAGATAAAATGACCATCTTGCCCTCAATTAATAATCTTCTCCATAGTGTGTTAGCATGAAAAAGAGGTTACTATTTGATAATGCAGTTT[A/G]
TGGTGGGACTGAAAAAAAAAAGCCAAACTTACCTATAAGATGACGAACAAATAAGTATTTTTTTAATATTATGGAAAACATTGAAACAATAATTTTTTAA

Reverse complement sequence

TTAAAAAATTATTGTTTCAATGTTTTCCATAATATTAAAAAAATACTTATTTGTTCGTCATCTTATAGGTAAGTTTGGCTTTTTTTTTTCAGTCCCACCA[T/C]
AAACTGCATTATCAAATAGTAACCTCTTTTTCATGCTAACACACTATGGAGAAGATTATTAATTGAGGGCAAGATGGTCATTTTATCTATCTCATTAATT

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 49.60% 47.40% 0.06% 2.92% NA
All Indica  2759 30.30% 66.90% 0.11% 2.68% NA
All Japonica  1512 88.60% 11.10% 0.00% 0.26% NA
Aus  269 39.40% 60.60% 0.00% 0.00% NA
Indica I  595 35.60% 64.40% 0.00% 0.00% NA
Indica II  465 7.70% 92.00% 0.22% 0.00% NA
Indica III  913 41.40% 52.60% 0.11% 5.91% NA
Indica Intermediate  786 26.60% 70.70% 0.13% 2.54% NA
Temperate Japonica  767 96.50% 3.40% 0.00% 0.13% NA
Tropical Japonica  504 76.60% 23.40% 0.00% 0.00% NA
Japonica Intermediate  241 88.80% 10.00% 0.00% 1.24% NA
VI/Aromatic  96 26.00% 17.70% 0.00% 56.25% NA
Intermediate  90 41.10% 52.20% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0808948492 A -> G LOC_Os08g14850.1 intron_variant ; MODIFIER silent_mutation Average:35.498; most accessible tissue: Callus, score: 59.961 N N N N
vg0808948492 A -> DEL N N silent_mutation Average:35.498; most accessible tissue: Callus, score: 59.961 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808948492 NA 1.42E-09 mr1180 Ind_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
vg0808948492 NA 2.87E-08 mr1183 Ind_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
vg0808948492 NA 6.77E-07 mr1418 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
vg0808948492 NA 4.13E-08 mr1503 Ind_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
vg0808948492 NA 2.94E-08 mr1063_2 Ind_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
vg0808948492 NA 6.42E-12 mr1180_2 Ind_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
vg0808948492 NA 6.65E-12 mr1183_2 Ind_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