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Detailed information for vg1004566041:

Variant ID: vg1004566041 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4566041
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, T: 0.07, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGACCTCAACAAATATATTTTGTTTGTGCATATTTGATTGTTGCTTGAATATTGGTTTTTTTTTCTCGCGTATTCTAGACTGTGTATCGGTTAGTCGT[G/T]
AGGCAACGTATGCAGCTTCCAGGAGGTGAAGGTTGATCAAGATTATATTAAGAATAAGAACTACTCTGAGCAGGCAAGTCATCACTATTCCTTGCACATG

Reverse complement sequence

CATGTGCAAGGAATAGTGATGACTTGCCTGCTCAGAGTAGTTCTTATTCTTAATATAATCTTGATCAACCTTCACCTCCTGGAAGCTGCATACGTTGCCT[C/A]
ACGACTAACCGATACACAGTCTAGAATACGCGAGAAAAAAAAACCAATATTCAAGCAACAATCAAATATGCACAAACAAAATATATTTGTTGAGGTCGAA

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	93.30%	3.40%	3.32%	0.00%	NA
All Indica	2759	95.90%	0.50%	3.55%	0.00%	NA
All Japonica	1512	89.20%	7.80%	3.04%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	99.10%	0.20%	0.65%	0.00%	NA
Indica III	913	91.10%	1.00%	7.89%	0.00%	NA
Indica Intermediate	786	96.90%	0.10%	2.93%	0.00%	NA
Temperate Japonica	767	84.50%	14.60%	0.91%	0.00%	NA
Tropical Japonica	504	92.70%	0.00%	7.34%	0.00%	NA
Japonica Intermediate	241	96.70%	2.50%	0.83%	0.00%	NA
VI/Aromatic	96	63.50%	26.00%	10.42%	0.00%	NA
Intermediate	90	95.60%	3.30%	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
vg1004566041	G -> T	LOC_Os10g08400.1	upstream_gene_variant ; 2042.0bp to feature; MODIFIER	silent_mutation	Average:21.776; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1004566041	G -> T	LOC_Os10g08410.1	upstream_gene_variant ; 3101.0bp to feature; MODIFIER	silent_mutation	Average:21.776; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg1004566041	G -> T	LOC_Os10g08400-LOC_Os10g08410	intergenic_region ; MODIFIER	silent_mutation	Average:21.776; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004566041	5.08E-06	NA	mr1241	Jap_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
vg1004566041	2.73E-07	2.73E-07	mr1973	Jap_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
vg1004566041	NA	2.05E-08	mr1062_2	Jap_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