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Detailed information for vg1001586279:

Variant ID: vg1001586279 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1586279
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGTGAAAATTAACCTAAGATTTGTTTGTACCGGGCGATGTCGTCATTCTGTCGGCATGTCCTTATCGAAGACTTTGTCTTATGAGTTTTCCCTTGATG[G/A]
ACCACTGATCTTTGTATGTGGGTATCGCGGTCTGCGTGGTTAGCTCACTTTGATAATGTCAAGCTTGTTGTCGTTTTTCCTTAATTAACTATGTTGTTGA

Reverse complement sequence

TCAACAACATAGTTAATTAAGGAAAAACGACAACAAGCTTGACATTATCAAAGTGAGCTAACCACGCAGACCGCGATACCCACATACAAAGATCAGTGGT[C/T]
CATCAAGGGAAAACTCATAAGACAAAGTCTTCGATAAGGACATGCCGACAGAATGACGACATCGCCCGGTACAAACAAATCTTAGGTTAATTTTCACCCG

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	36.50%	19.10%	1.63%	42.76%	NA
All Indica	2759	5.70%	30.60%	2.50%	61.18%	NA
All Japonica	1512	94.10%	0.70%	0.26%	4.89%	NA
Aus	269	5.20%	9.70%	0.74%	84.39%	NA
Indica I	595	3.00%	41.80%	1.85%	53.28%	NA
Indica II	465	6.90%	31.20%	3.66%	58.28%	NA
Indica III	913	4.60%	26.60%	2.63%	66.16%	NA
Indica Intermediate	786	8.30%	26.50%	2.16%	63.10%	NA
Temperate Japonica	767	98.20%	0.40%	0.13%	1.30%	NA
Tropical Japonica	504	86.70%	1.20%	0.60%	11.51%	NA
Japonica Intermediate	241	96.70%	0.80%	0.00%	2.49%	NA
VI/Aromatic	96	88.50%	1.00%	0.00%	10.42%	NA
Intermediate	90	52.20%	21.10%	2.22%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001586279	G -> A	LOC_Os10g03640.1	downstream_gene_variant ; 1579.0bp to feature; MODIFIER	silent_mutation	Average:23.186; most accessible tissue: Callus, score: 65.629	N	N	N	N
vg1001586279	G -> A	LOC_Os10g03630-LOC_Os10g03640	intergenic_region ; MODIFIER	silent_mutation	Average:23.186; most accessible tissue: Callus, score: 65.629	N	N	N	N
vg1001586279	G -> DEL	N	N	silent_mutation	Average:23.186; most accessible tissue: Callus, score: 65.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001586279	NA	4.90E-09	mr1486	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
vg1001586279	NA	1.60E-06	mr1548	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
vg1001586279	NA	3.15E-06	mr1721	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
vg1001586279	9.13E-06	NA	mr1168_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
vg1001586279	7.33E-07	5.36E-08	mr1168_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
vg1001586279	NA	2.54E-09	mr1486_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
vg1001586279	NA	9.19E-07	mr1721_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