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Detailed information for vg0915200017:

Variant ID: vg0915200017 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 15200017
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GAAAGAAATTTCCATATAAGAACCCAATACGAGATTAATCAAAATTCAAAATAAAAAAAAATAAAATCCAAAATTAGAAAAGAAAATGAGAGTCCAAGTA[G/A]
GAATACAATTTAAAATTAGCTGAAATTAGAAATTAAAAATAAGGAATATTAAAAGAAGAGTCCATATAAGAACCAAATACGAGATTAATTAAAATTCAGA

Reverse complement sequence

TCTGAATTTTAATTAATCTCGTATTTGGTTCTTATATGGACTCTTCTTTTAATATTCCTTATTTTTAATTTCTAATTTCAGCTAATTTTAAATTGTATTC[C/T]
TACTTGGACTCTCATTTTCTTTTCTAATTTTGGATTTTATTTTTTTTTATTTTGAATTTTGATTAATCTCGTATTGGGTTCTTATATGGAAATTTCTTTC

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	66.90%	32.40%	0.59%	0.15%	NA
All Indica	2759	48.60%	50.20%	0.94%	0.25%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	50.60%	49.40%	0.00%	0.00%	NA
Indica I	595	42.40%	57.50%	0.17%	0.00%	NA
Indica II	465	63.40%	35.90%	0.43%	0.22%	NA
Indica III	913	39.80%	57.80%	1.86%	0.55%	NA
Indica Intermediate	786	54.80%	44.30%	0.76%	0.13%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	88.90%	10.00%	1.11%	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
vg0915200017	G -> DEL	N	N	silent_mutation	Average:17.194; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0915200017	G -> A	LOC_Os09g25370.1	downstream_gene_variant ; 4116.0bp to feature; MODIFIER	silent_mutation	Average:17.194; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0915200017	G -> A	LOC_Os09g25360-LOC_Os09g25370	intergenic_region ; MODIFIER	silent_mutation	Average:17.194; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0915200017	NA	8.80E-06	mr1007	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
vg0915200017	NA	4.23E-07	mr1006_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
vg0915200017	1.23E-06	NA	mr1010_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
vg0915200017	7.20E-06	3.57E-09	mr1010_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
vg0915200017	NA	6.25E-06	mr1968_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