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Detailed information for vg0712084027:

Variant ID: vg0712084027 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12084027
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, C: 0.07, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

ACAACCATCAAAACCATGTGCTCATAACCCACCCTTAATCAGGTTTTAATTATCAATTAATTATCATAACACGATTAACCATCGTGAGCTACCATTAAAT[C/A]
TAACCATAACTAATAATGTAATATGATTCATCCCATTAATGAACTAATGTTTCTAAGCATGGCTAAGCAATTATACCTATATAGCACACTTAGCTGAACC

Reverse complement sequence

GGTTCAGCTAAGTGTGCTATATAGGTATAATTGCTTAGCCATGCTTAGAAACATTAGTTCATTAATGGGATGAATCATATTACATTATTAGTTATGGTTA[G/T]
ATTTAATGGTAGCTCACGATGGTTAATCGTGTTATGATAATTAATTGATAATTAAAACCTGATTAAGGGTGGGTTATGAGCACATGGTTTTGATGGTTGT

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	13.60%	6.80%	31.91%	47.71%	NA
All Indica	2759	3.20%	9.10%	39.69%	48.02%	NA
All Japonica	1512	32.90%	3.20%	15.67%	48.28%	NA
Aus	269	11.20%	6.30%	45.35%	37.17%	NA
Indica I	595	2.90%	4.00%	20.50%	72.61%	NA
Indica II	465	4.50%	6.00%	37.63%	51.83%	NA
Indica III	913	0.70%	15.00%	57.06%	27.27%	NA
Indica Intermediate	786	5.70%	7.80%	35.24%	51.27%	NA
Temperate Japonica	767	51.20%	0.40%	1.83%	46.54%	NA
Tropical Japonica	504	11.30%	7.70%	35.52%	45.44%	NA
Japonica Intermediate	241	19.50%	2.50%	18.26%	59.75%	NA
VI/Aromatic	96	7.30%	3.10%	29.17%	60.42%	NA
Intermediate	90	21.10%	3.30%	28.89%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712084027	C -> DEL	N	N	silent_mutation	Average:17.861; most accessible tissue: Callus, score: 29.175	N	N	N	N
vg0712084027	C -> A	LOC_Os07g20880.1	upstream_gene_variant ; 1318.0bp to feature; MODIFIER	silent_mutation	Average:17.861; most accessible tissue: Callus, score: 29.175	N	N	N	N
vg0712084027	C -> A	LOC_Os07g20890.1	upstream_gene_variant ; 419.0bp to feature; MODIFIER	silent_mutation	Average:17.861; most accessible tissue: Callus, score: 29.175	N	N	N	N
vg0712084027	C -> A	LOC_Os07g20880-LOC_Os07g20890	intergenic_region ; MODIFIER	silent_mutation	Average:17.861; most accessible tissue: Callus, score: 29.175	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712084027	NA	3.86E-09	mr1660	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
vg0712084027	2.95E-06	2.95E-06	mr1786	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