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Detailed information for vg0600912720:

Variant ID: vg0600912720 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 912720
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

TGTCTGGCATGTGACATTTTTACATAATCAATAAAATCTTGAATCTCAAAGGAAAAAAAATTACATGTAAGATGATATCAGATGTTCATATTGGTACCAT[G/A]
TCAACATAGATACTGTAATATTGTAATTTTTCGTTTTTCTGGTTACGACTTATCAGGGTTGTATCAATATGAACTTCGCACTATGTTACGTGAGTCGTTA

Reverse complement sequence

TAACGACTCACGTAACATAGTGCGAAGTTCATATTGATACAACCCTGATAAGTCGTAACCAGAAAAACGAAAAATTACAATATTACAGTATCTATGTTGA[C/T]
ATGGTACCAATATGAACATCTGATATCATCTTACATGTAATTTTTTTTCCTTTGAGATTCAAGATTTTATTGATTATGTAAAAATGTCACATGCCAGACA

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	61.30%	38.60%	0.13%	0.00%	NA
All Indica	2759	49.40%	50.50%	0.11%	0.00%	NA
All Japonica	1512	92.20%	7.70%	0.13%	0.00%	NA
Aus	269	23.00%	77.00%	0.00%	0.00%	NA
Indica I	595	70.90%	29.10%	0.00%	0.00%	NA
Indica II	465	59.40%	40.60%	0.00%	0.00%	NA
Indica III	913	29.70%	70.20%	0.11%	0.00%	NA
Indica Intermediate	786	50.30%	49.50%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	79.00%	20.80%	0.20%	0.00%	NA
Japonica Intermediate	241	95.40%	4.10%	0.41%	0.00%	NA
VI/Aromatic	96	15.60%	84.40%	0.00%	0.00%	NA
Intermediate	90	68.90%	30.00%	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
vg0600912720	G -> A	LOC_Os06g02580.1	upstream_gene_variant ; 2398.0bp to feature; MODIFIER	silent_mutation	Average:43.638; most accessible tissue: Callus, score: 80.673	N	N	N	N
vg0600912720	G -> A	LOC_Os06g02590.1	upstream_gene_variant ; 1059.0bp to feature; MODIFIER	silent_mutation	Average:43.638; most accessible tissue: Callus, score: 80.673	N	N	N	N
vg0600912720	G -> A	LOC_Os06g02580-LOC_Os06g02590	intergenic_region ; MODIFIER	silent_mutation	Average:43.638; most accessible tissue: Callus, score: 80.673	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0600912720	NA	3.05E-08	mr1063	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
vg0600912720	NA	1.43E-07	mr1583	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
vg0600912720	NA	1.44E-10	mr1870	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
vg0600912720	NA	4.44E-08	mr1870_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