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Detailed information for vg0713357787:

Variant ID: vg0713357787 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13357787
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, A: 0.29, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TGGTTGGATATATCAACACTAAAATCCAAATAGGATAATATACGGCATGAAACTTAAATAGACATGTAATCCAAATAGGTAACAGCACGGTTTTCACTAA[C/A]
CATGCAGTTACTGTGATAACCACCTTACCATGGAAGTGGCAGTAACCGTACCCCACCCAAAACAGTTTGGTGATTAGAGGGGTTTGTCCCTTTTTTTTCA

Reverse complement sequence

TGAAAAAAAAGGGACAAACCCCTCTAATCACCAAACTGTTTTGGGTGGGGTACGGTTACTGCCACTTCCATGGTAAGGTGGTTATCACAGTAACTGCATG[G/T]
TTAGTGAAAACCGTGCTGTTACCTATTTGGATTACATGTCTATTTAAGTTTCATGCCGTATATTATCCTATTTGGATTTTAGTGTTGATATATCCAACCA

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	34.40%	10.20%	1.12%	54.25%	NA
All Indica	2759	20.00%	0.40%	1.01%	78.62%	NA
All Japonica	1512	65.30%	28.40%	0.20%	6.08%	NA
Aus	269	16.70%	3.00%	1.12%	79.18%	NA
Indica I	595	34.80%	0.00%	2.18%	63.03%	NA
Indica II	465	14.40%	0.40%	0.86%	84.30%	NA
Indica III	913	6.20%	0.20%	0.44%	93.10%	NA
Indica Intermediate	786	28.10%	0.80%	0.89%	70.23%	NA
Temperate Japonica	767	63.10%	35.50%	0.00%	1.43%	NA
Tropical Japonica	504	82.10%	4.20%	0.00%	13.69%	NA
Japonica Intermediate	241	36.90%	56.80%	1.24%	4.98%	NA
VI/Aromatic	96	4.20%	29.20%	14.58%	52.08%	NA
Intermediate	90	43.30%	6.70%	5.56%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713357787	C -> DEL	N	N	silent_mutation	Average:45.534; most accessible tissue: Callus, score: 77.504	N	N	N	N
vg0713357787	C -> A	LOC_Os07g23640.1	upstream_gene_variant ; 2490.0bp to feature; MODIFIER	silent_mutation	Average:45.534; most accessible tissue: Callus, score: 77.504	N	N	N	N
vg0713357787	C -> A	LOC_Os07g23630.1	downstream_gene_variant ; 4291.0bp to feature; MODIFIER	silent_mutation	Average:45.534; most accessible tissue: Callus, score: 77.504	N	N	N	N
vg0713357787	C -> A	LOC_Os07g23640-LOC_Os07g23660	intergenic_region ; MODIFIER	silent_mutation	Average:45.534; most accessible tissue: Callus, score: 77.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713357787	4.28E-06	NA	mr1270	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
vg0713357787	NA	2.60E-06	mr1705	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