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Detailed information for vg0706605860:

Variant ID: vg0706605860 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6605860
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, G: 0.10, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

ATATCTGTCCTGCCAAAGATAGAAGCATATAATGATGTTAAATGATGCGTAGGGTTTAGCATATAAGTATGTTAAATGATCTTCACATAAGTATTTTAAT[G/C]
TACTGATGCATAGGGTTTAGCATATAAGTATGTTAAATGATCATCCTCACATCATTTTTTATAGTATTTTAATATTTATAATTTCTATAATATTTAACAT

Reverse complement sequence

ATGTTAAATATTATAGAAATTATAAATATTAAAATACTATAAAAAATGATGTGAGGATGATCATTTAACATACTTATATGCTAAACCCTATGCATCAGTA[C/G]
ATTAAAATACTTATGTGAAGATCATTTAACATACTTATATGCTAAACCCTACGCATCATTTAACATCATTATATGCTTCTATCTTTGGCAGGACAGATAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.20%	18.90%	0.87%	42.07%	NA
All Indica	2759	8.40%	23.00%	1.30%	67.34%	NA
All Japonica	1512	93.30%	0.20%	0.26%	6.28%	NA
Aus	269	7.80%	86.60%	0.37%	5.20%	NA
Indica I	595	11.10%	26.60%	1.51%	60.84%	NA
Indica II	465	12.90%	5.20%	1.51%	80.43%	NA
Indica III	913	2.50%	25.10%	1.53%	70.87%	NA
Indica Intermediate	786	10.40%	28.40%	0.76%	60.43%	NA
Temperate Japonica	767	88.00%	0.30%	0.52%	11.21%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	97.10%	0.40%	0.00%	2.49%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	58.90%	17.80%	0.00%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706605860	G -> DEL	N	N	silent_mutation	Average:9.764; most accessible tissue: Callus, score: 47.451	N	N	N	N
vg0706605860	G -> C	LOC_Os07g11890.1	downstream_gene_variant ; 2393.0bp to feature; MODIFIER	silent_mutation	Average:9.764; most accessible tissue: Callus, score: 47.451	N	N	N	N
vg0706605860	G -> C	LOC_Os07g11900.1	downstream_gene_variant ; 3264.0bp to feature; MODIFIER	silent_mutation	Average:9.764; most accessible tissue: Callus, score: 47.451	N	N	N	N
vg0706605860	G -> C	LOC_Os07g11890-LOC_Os07g11900	intergenic_region ; MODIFIER	silent_mutation	Average:9.764; most accessible tissue: Callus, score: 47.451	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706605860	2.90E-06	2.90E-06	mr1640	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