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Detailed information for vg0107884262:

Variant ID: vg0107884262 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7884262
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


ACCCGGCGGAGTGGGGGTGGGTATGACCCGTCACGTCCGAGCGTCACTCGAGGAAGGGCTGTCACAGGTCATCGTTCATTTATGAGGGAATGACAGGGCT[G/A]
TCCACCGTGTCAGGCGGGGGCCGGCACCTGGTTCCACTCGAGAACCGGTTGTTGCTTAGCTTCCGGGAGAAGGCACGATTTAAAGCCCAGGAAAAGTGGA

Reverse complement sequence

TCCACTTTTCCTGGGCTTTAAATCGTGCCTTCTCCCGGAAGCTAAGCAACAACCGGTTCTCGAGTGGAACCAGGTGCCGGCCCCCGCCTGACACGGTGGA[C/T]
AGCCCTGTCATTCCCTCATAAATGAACGATGACCTGTGACAGCCCTTCCTCGAGTGACGCTCGGACGTGACGGGTCATACCCACCCCCACTCCGCCGGGT

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 92.40% 7.50% 0.04% 0.00% NA
All Indica  2759 95.70% 4.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 13.80% 85.50% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 93.00% 7.00% 0.00% 0.00% NA
Indica Intermediate  786 94.50% 5.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 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
vg0107884262 G -> A LOC_Os01g14080.1 upstream_gene_variant ; 1630.0bp to feature; MODIFIER silent_mutation Average:74.615; most accessible tissue: Minghui63 flower, score: 83.947 N N N N
vg0107884262 G -> A LOC_Os01g14080-LOC_Os01g14090 intergenic_region ; MODIFIER silent_mutation Average:74.615; most accessible tissue: Minghui63 flower, score: 83.947 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107884262 3.18E-06 NA mr1158 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
vg0107884262 NA 1.09E-06 mr1286 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
vg0107884262 NA 1.70E-08 mr1465 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
vg0107884262 NA 5.08E-06 mr1777 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