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Detailed information for vg1005865739:

Variant ID: vg1005865739 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5865739
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

ACATCTACCAGAAAATATATTACTTATTAGCTAACCATCCCCTGCACATCTACCAGAAAATATATTACTTATTAGCTAACCATACCATATTACTTACTAC[C/A]
AGAAAATATATTACTTATTAGCTAACCATACCCCGTCCACATGTCCACAACCCCAGGTAGACACATTGCTTTACTTATTAGCTAACCATACCCCGTCCAC

Reverse complement sequence

GTGGACGGGGTATGGTTAGCTAATAAGTAAAGCAATGTGTCTACCTGGGGTTGTGGACATGTGGACGGGGTATGGTTAGCTAATAAGTAATATATTTTCT[G/T]
GTAGTAAGTAATATGGTATGGTTAGCTAATAAGTAATATATTTTCTGGTAGATGTGCAGGGGATGGTTAGCTAATAAGTAATATATTTTCTGGTAGATGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.80%	10.30%	2.56%	2.37%	NA
All Indica	2759	75.80%	17.10%	4.35%	2.72%	NA
All Japonica	1512	97.40%	0.30%	0.00%	2.31%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	91.10%	5.70%	2.69%	0.50%	NA
Indica II	465	72.00%	19.10%	4.73%	4.09%	NA
Indica III	913	72.50%	20.30%	3.40%	3.83%	NA
Indica Intermediate	786	70.20%	21.00%	6.49%	2.29%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	93.10%	0.20%	0.00%	6.75%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	8.90%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005865739	C -> A	LOC_Os10g10610.1	upstream_gene_variant ; 1101.0bp to feature; MODIFIER	silent_mutation	Average:63.034; most accessible tissue: Minghui63 root, score: 80.951	N	N	N	N
vg1005865739	C -> A	LOC_Os10g10620.1	downstream_gene_variant ; 803.0bp to feature; MODIFIER	silent_mutation	Average:63.034; most accessible tissue: Minghui63 root, score: 80.951	N	N	N	N
vg1005865739	C -> A	LOC_Os10g10610-LOC_Os10g10620	intergenic_region ; MODIFIER	silent_mutation	Average:63.034; most accessible tissue: Minghui63 root, score: 80.951	N	N	N	N
vg1005865739	C -> DEL	N	N	silent_mutation	Average:63.034; most accessible tissue: Minghui63 root, score: 80.951	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005865739	3.80E-06	2.98E-12	mr1027_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
vg1005865739	NA	6.26E-06	mr1057_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
vg1005865739	NA	3.36E-11	mr1580_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
vg1005865739	1.02E-06	2.90E-12	mr1825_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
vg1005865739	NA	2.32E-06	mr1943_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