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Detailed information for vg0315165022:

Variant ID: vg0315165022 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15165022
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.24, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTTGGAGGGGTTGGGAACCCCTCCCCTCCACACGCAAAATGGAGCGATAGATTAACGCATGGTTAATTAAGTATTAACTATAAAAAACTTTAAAAAAT[G/A]
GATTAATATAATTTTTAAAGCAACTTTTTTTTGGCAAAAAAACACACCGTTTAGCCGTTTGAAAAGTGTGCGCGTGCGAGGGAGGTGAGTTGGGAAAGTT

Reverse complement sequence

AACTTTCCCAACTCACCTCCCTCGCACGCGCACACTTTTCAAACGGCTAAACGGTGTGTTTTTTTGCCAAAAAAAAGTTGCTTTAAAAATTATATTAATC[C/T]
ATTTTTTAAAGTTTTTTATAGTTAATACTTAATTAACCATGCGTTAATCTATCGCTCCATTTTGCGTGTGGAGGGGAGGGGTTCCCAACCCCTCCAAAAG

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	88.20%	9.70%	0.34%	1.74%	NA
All Indica	2759	91.40%	5.20%	0.54%	2.90%	NA
All Japonica	1512	87.30%	12.60%	0.07%	0.00%	NA
Aus	269	84.40%	15.60%	0.00%	0.00%	NA
Indica I	595	94.30%	3.50%	0.84%	1.34%	NA
Indica II	465	91.80%	0.60%	0.43%	7.10%	NA
Indica III	913	89.00%	9.10%	0.33%	1.53%	NA
Indica Intermediate	786	91.60%	4.60%	0.64%	3.18%	NA
Temperate Japonica	767	96.00%	4.00%	0.00%	0.00%	NA
Tropical Japonica	504	88.70%	11.10%	0.20%	0.00%	NA
Japonica Intermediate	241	56.80%	43.20%	0.00%	0.00%	NA
VI/Aromatic	96	26.00%	74.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	13.30%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315165022	G -> A	LOC_Os03g26550.1	upstream_gene_variant ; 439.0bp to feature; MODIFIER	silent_mutation	Average:53.141; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0315165022	G -> A	LOC_Os03g26560.1	upstream_gene_variant ; 3379.0bp to feature; MODIFIER	silent_mutation	Average:53.141; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0315165022	G -> A	LOC_Os03g26540-LOC_Os03g26550	intergenic_region ; MODIFIER	silent_mutation	Average:53.141; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0315165022	G -> DEL	N	N	silent_mutation	Average:53.141; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315165022	NA	7.25E-06	mr1180	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
vg0315165022	NA	4.86E-06	mr1114_2	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
vg0315165022	NA	3.26E-07	mr1117_2	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
vg0315165022	NA	9.06E-07	mr1119_2	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
vg0315165022	NA	6.62E-06	mr1120_2	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
vg0315165022	NA	4.77E-06	mr1123_2	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
vg0315165022	NA	5.95E-07	mr1240_2	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
vg0315165022	NA	7.59E-06	mr1242_2	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
vg0315165022	NA	2.44E-06	mr1247_2	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
vg0315165022	NA	1.40E-07	mr1496_2	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
vg0315165022	2.68E-06	NA	mr1961_2	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
vg0315165022	NA	8.00E-07	mr1961_2	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