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Detailed information for vg0805969903:

Variant ID: vg0805969903 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5969903
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

CTGATCAAGCGACCCTTCTCTATATAAACCGACCTGCCGTCTTCACGCAACGCACGCAAAATCAATCTAGGGTTTGCCTCCTACTCTATGCTGCACCGTC[G/A]
CTCGTAGATTACTCCATCGCGCTCGTCGGCGTGCACTGGCGATCGGGAGAGCAGGTCTCTTGAACCTCTGCCTTCGATGTCCTGCACCGAGAGAAGGCGA

Reverse complement sequence

TCGCCTTCTCTCGGTGCAGGACATCGAAGGCAGAGGTTCAAGAGACCTGCTCTCCCGATCGCCAGTGCACGCCGACGAGCGCGATGGAGTAATCTACGAG[C/T]
GACGGTGCAGCATAGAGTAGGAGGCAAACCCTAGATTGATTTTGCGTGCGTTGCGTGAAGACGGCAGGTCGGTTTATATAGAGAAGGGTCGCTTGATCAG

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	74.00%	21.10%	0.91%	4.08%	NA
All Indica	2759	57.00%	35.30%	0.98%	6.67%	NA
All Japonica	1512	99.10%	0.20%	0.26%	0.46%	NA
Aus	269	94.40%	1.50%	4.09%	0.00%	NA
Indica I	595	57.50%	40.80%	0.84%	0.84%	NA
Indica II	465	51.00%	46.70%	0.22%	2.15%	NA
Indica III	913	56.20%	30.20%	1.10%	12.49%	NA
Indica Intermediate	786	61.20%	30.40%	1.40%	7.00%	NA
Temperate Japonica	767	99.50%	0.30%	0.13%	0.13%	NA
Tropical Japonica	504	98.80%	0.00%	0.00%	1.19%	NA
Japonica Intermediate	241	98.30%	0.40%	1.24%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	85.60%	12.20%	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
vg0805969903	G -> A	LOC_Os08g10260.1	upstream_gene_variant ; 2056.0bp to feature; MODIFIER	silent_mutation	Average:66.91; most accessible tissue: Zhenshan97 flag leaf, score: 83.84	N	N	N	N
vg0805969903	G -> A	LOC_Os08g10270.1	upstream_gene_variant ; 527.0bp to feature; MODIFIER	silent_mutation	Average:66.91; most accessible tissue: Zhenshan97 flag leaf, score: 83.84	N	N	N	N
vg0805969903	G -> A	LOC_Os08g10260-LOC_Os08g10270	intergenic_region ; MODIFIER	silent_mutation	Average:66.91; most accessible tissue: Zhenshan97 flag leaf, score: 83.84	N	N	N	N
vg0805969903	G -> DEL	N	N	silent_mutation	Average:66.91; most accessible tissue: Zhenshan97 flag leaf, score: 83.84	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805969903	NA	3.01E-06	mr1212	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
vg0805969903	NA	1.60E-16	mr1352_2	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
vg0805969903	NA	2.44E-06	mr1380_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
vg0805969903	1.34E-07	1.34E-07	mr1615_2	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