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Detailed information for vg0200800465:

Variant ID: vg0200800465 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 800465
Reference Allele: A	Alternative Allele: G
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: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAGATGAATATCTTTAGTCCCGGATCCGTACTCCCGGTTGGAAAACCGGGATTAAAGGGGGTTCCCAACCGGGAGTAAAGATGGTTTCTCCACCAGTG[A/G]
CATGTGCATGCAGTGCAGTGTGATACCGAAACCTTTTTTCAGGAAAATGTGTAGTTTTCATGAATAAATCTCAGATGTATATTTTTTTATTTAATGGTAG

Reverse complement sequence

CTACCATTAAATAAAAAAATATACATCTGAGATTTATTCATGAAAACTACACATTTTCCTGAAAAAAGGTTTCGGTATCACACTGCACTGCATGCACATG[T/C]
CACTGGTGGAGAAACCATCTTTACTCCCGGTTGGGAACCCCCTTTAATCCCGGTTTTCCAACCGGGAGTACGGATCCGGGACTAAAGATATTCATCTTTA

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	61.40%	38.50%	0.11%	0.00%	NA
All Indica	2759	93.50%	6.50%	0.04%	0.00%	NA
All Japonica	1512	6.00%	94.00%	0.07%	0.00%	NA
Aus	269	68.40%	31.20%	0.37%	0.00%	NA
Indica I	595	98.50%	1.30%	0.17%	0.00%	NA
Indica II	465	78.50%	21.50%	0.00%	0.00%	NA
Indica III	913	98.40%	1.60%	0.00%	0.00%	NA
Indica Intermediate	786	92.90%	7.10%	0.00%	0.00%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	10.70%	89.30%	0.00%	0.00%	NA
Japonica Intermediate	241	13.30%	86.30%	0.41%	0.00%	NA
VI/Aromatic	96	15.60%	84.40%	0.00%	0.00%	NA
Intermediate	90	36.70%	61.10%	2.22%	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
vg0200800465	A -> G	LOC_Os02g02380.1	upstream_gene_variant ; 4185.0bp to feature; MODIFIER	silent_mutation	Average:50.513; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0200800465	A -> G	LOC_Os02g02380-LOC_Os02g02390	intergenic_region ; MODIFIER	silent_mutation	Average:50.513; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200800465	NA	8.17E-07	mr1278	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
vg0200800465	NA	1.36E-10	mr1325	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
vg0200800465	NA	4.30E-06	mr1450	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
vg0200800465	NA	3.57E-29	mr1638	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
vg0200800465	NA	2.61E-12	mr1667	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
vg0200800465	2.61E-07	2.92E-11	mr1680	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
vg0200800465	NA	1.20E-23	mr1698	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
vg0200800465	NA	2.89E-12	mr1744	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
vg0200800465	NA	1.60E-06	mr1796	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
vg0200800465	NA	3.62E-06	mr1990	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
vg0200800465	NA	2.94E-06	mr1042_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
vg0200800465	NA	9.64E-06	mr1269_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
vg0200800465	NA	3.44E-07	mr1568_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
vg0200800465	NA	2.98E-10	mr1756_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
vg0200800465	NA	1.17E-06	mr1871_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
vg0200800465	NA	4.57E-06	mr1928_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