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Detailed information for vg0113677789:

Variant ID: vg0113677789 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13677789
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 42. )

Flanking Sequence (100 bp) in Reference Genome:

CAGGGCCGGTCAGACCGCAGGTATATGGGCGGTCTGACCGGCTAGTAGGGCCGGTCTAACCGCTGGTATGTGGGCGGTCAGACCGTCAGGGTCCAAGTCC[G/A]
AGTCTGTTTTCGTCGGATCTCGGGTTTCCTTGCTCAGGAAGGCATGTTTCGTGTTTCCTTTGGTTTCTATCCCGAGTTGGACGTGGAGAAGGGCCTGTAG

Reverse complement sequence

CTACAGGCCCTTCTCCACGTCCAACTCGGGATAGAAACCAAAGGAAACACGAAACATGCCTTCCTGAGCAAGGAAACCCGAGATCCGACGAAAACAGACT[C/T]
GGACTTGGACCCTGACGGTCTGACCGCCCACATACCAGCGGTTAGACCGGCCCTACTAGCCGGTCAGACCGCCCATATACCTGCGGTCTGACCGGCCCTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.40%	5.10%	13.63%	38.87%	NA
All Indica	2759	21.80%	7.20%	20.48%	50.45%	NA
All Japonica	1512	84.40%	2.40%	1.72%	11.44%	NA
Aus	269	12.60%	0.40%	8.18%	78.81%	NA
Indica I	595	10.60%	15.10%	11.43%	62.86%	NA
Indica II	465	20.00%	2.80%	25.59%	51.61%	NA
Indica III	913	34.80%	1.20%	23.55%	40.42%	NA
Indica Intermediate	786	16.30%	10.90%	20.74%	52.04%	NA
Temperate Japonica	767	97.10%	1.20%	0.91%	0.78%	NA
Tropical Japonica	504	61.50%	5.00%	2.98%	30.56%	NA
Japonica Intermediate	241	91.70%	1.20%	1.66%	5.39%	NA
VI/Aromatic	96	45.80%	0.00%	20.83%	33.33%	NA
Intermediate	90	55.60%	1.10%	12.22%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113677789	G -> A	LOC_Os01g24280.1	upstream_gene_variant ; 590.0bp to feature; MODIFIER	silent_mutation	Average:7.852; most accessible tissue: Callus, score: 14.343	N	N	N	N
vg0113677789	G -> A	LOC_Os01g24270-LOC_Os01g24280	intergenic_region ; MODIFIER	silent_mutation	Average:7.852; most accessible tissue: Callus, score: 14.343	N	N	N	N
vg0113677789	G -> DEL	N	N	silent_mutation	Average:7.852; most accessible tissue: Callus, score: 14.343	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113677789	NA	9.25E-06	mr1136	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
vg0113677789	NA	9.18E-06	mr1316	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
vg0113677789	NA	9.85E-06	mr1510	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
vg0113677789	4.76E-06	NA	mr1729	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
vg0113677789	NA	2.41E-06	mr1741	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