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Detailed information for vg1003779182:

Variant ID: vg1003779182 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3779182
Reference Allele: G	Alternative Allele: T,A
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

CGGACCCAACAAAAACAGTAACCCTGTTCATCACCTGAAAAATCAATCATCTCCAAAACCACTTCGCCAATAATCTCCAATATCAAAACCAATAATCACA[G/T,A]
ATGCCAATTGTTCATCACAAAATAAAGAATGAAAAACACTTTGATTTTACACGATGGAGATCGTATGACTCAATGAGCCACTCTTCGATTCCGTAAATCT

Reverse complement sequence

AGATTTACGGAATCGAAGAGTGGCTCATTGAGTCATACGATCTCCATCGTGTAAAATCAAAGTGTTTTTCATTCTTTATTTTGTGATGAACAATTGGCAT[C/A,T]
TGTGATTATTGGTTTTGATATTGGAGATTATTGGCGAAGTGGTTTTGGAGATGATTGATTTTTCAGGTGATGAACAGGGTTACTGTTTTTGTTGGGTCCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.70%	2.20%	0.78%	20.72%	A: 0.61%
All Indica	2759	58.80%	3.70%	1.34%	35.12%	A: 1.05%
All Japonica	1512	99.80%	0.00%	0.00%	0.20%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	68.10%	0.00%	1.18%	30.59%	A: 0.17%
Indica II	465	66.70%	0.60%	1.94%	30.75%	NA
Indica III	913	41.90%	8.20%	1.42%	45.89%	A: 2.52%
Indica Intermediate	786	66.70%	3.10%	1.02%	28.63%	A: 0.64%
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	2.20%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003779182	G -> T	LOC_Os10g07190.1	upstream_gene_variant ; 1232.0bp to feature; MODIFIER	silent_mutation	Average:28.392; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg1003779182	G -> T	LOC_Os10g07200.1	downstream_gene_variant ; 457.0bp to feature; MODIFIER	silent_mutation	Average:28.392; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg1003779182	G -> T	LOC_Os10g07190-LOC_Os10g07200	intergenic_region ; MODIFIER	silent_mutation	Average:28.392; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg1003779182	G -> A	LOC_Os10g07190.1	upstream_gene_variant ; 1232.0bp to feature; MODIFIER	silent_mutation	Average:28.392; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg1003779182	G -> A	LOC_Os10g07200.1	downstream_gene_variant ; 457.0bp to feature; MODIFIER	silent_mutation	Average:28.392; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg1003779182	G -> A	LOC_Os10g07190-LOC_Os10g07200	intergenic_region ; MODIFIER	silent_mutation	Average:28.392; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N
vg1003779182	G -> DEL	N	N	silent_mutation	Average:28.392; most accessible tissue: Minghui63 root, score: 43.505	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003779182	NA	9.65E-06	mr1685	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
vg1003779182	3.73E-06	1.64E-06	mr1685	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