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Detailed information for vg0810228654:

Variant ID: vg0810228654 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10228654
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


CTTAGATTCCGGCTCTCCCAACGCTCTGGTGTACTTTGAAATAGTCGCCGAGGTTCCTCCAGCAGCAGAGCAAGGCAAGTCATGCTTGTCACTTGAACAT[G/A]
TTGATCCTATATTACAAATGCTCTACCGTTTTCCCTTAAATACTGCATTGCTTTATAATGATACTATGGGATGTTTACCTACTGTTACAGCCATGCTACT

Reverse complement sequence

AGTAGCATGGCTGTAACAGTAGGTAAACATCCCATAGTATCATTATAAAGCAATGCAGTATTTAAGGGAAAACGGTAGAGCATTTGTAATATAGGATCAA[C/T]
ATGTTCAAGTGACAAGCATGACTTGCCTTGCTCTGCTGCTGGAGGAACCTCGGCGACTATTTCAAAGTACACCAGAGCGTTGGGAGAGCCGGAATCTAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.50% 1.40% 0.19% 0.00% NA
All Indica  2759 99.50% 0.20% 0.29% 0.00% NA
All Japonica  1512 96.10% 3.80% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.40% 0.90% 1.72% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 92.30% 7.60% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0810228654 G -> A LOC_Os08g16730.1 upstream_gene_variant ; 835.0bp to feature; MODIFIER silent_mutation Average:47.408; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N
vg0810228654 G -> A LOC_Os08g16740.1 upstream_gene_variant ; 3849.0bp to feature; MODIFIER silent_mutation Average:47.408; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N
vg0810228654 G -> A LOC_Os08g16730-LOC_Os08g16740 intergenic_region ; MODIFIER silent_mutation Average:47.408; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810228654 NA 2.44E-07 mr1028 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
vg0810228654 5.45E-06 5.45E-06 mr1369 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
vg0810228654 NA 5.89E-07 mr1453 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
vg0810228654 NA 1.71E-06 mr1652 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
vg0810228654 NA 5.51E-06 mr1697 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
vg0810228654 2.89E-06 4.16E-07 mr1671_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