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Detailed information for vg1217187746:

Variant ID: vg1217187746 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17187746
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGATGCAAGGGTCAACCACTCTAACTATAAGTTATACTTCCCAAGAGAACCAATTTATCCCGCTTGACATGCTTTGACGTCTTCCCGAATGACGTTGCT[G/A]
CTGGACTTGTTATTGTCTGATCGTGATCCTGCCAGATCTGAAGCTTCGTTGTTAGAGGTGATTTTAATCTGACCTTTGTAGACTATCTTCGAACATATCA

Reverse complement sequence

TGATATGTTCGAAGATAGTCTACAAAGGTCAGATTAAAATCACCTCTAACAACGAAGCTTCAGATCTGGCAGGATCACGATCAGACAATAACAAGTCCAG[C/T]
AGCAACGTCATTCGGGAAGACGTCAAAGCATGTCAAGCGGGATAAATTGGTTCTCTTGGGAAGTATAACTTATAGTTAGAGTGGTTGACCCTTGCATCGA

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	41.80%	1.40%	18.28%	38.55%	NA
All Indica	2759	22.10%	0.00%	24.76%	53.14%	NA
All Japonica	1512	75.40%	4.20%	9.19%	11.24%	NA
Aus	269	41.30%	0.00%	7.81%	50.93%	NA
Indica I	595	17.50%	0.00%	29.92%	52.61%	NA
Indica II	465	25.80%	0.00%	18.92%	55.27%	NA
Indica III	913	17.40%	0.00%	25.19%	57.39%	NA
Indica Intermediate	786	28.90%	0.00%	23.79%	47.33%	NA
Temperate Japonica	767	81.00%	5.50%	8.08%	5.48%	NA
Tropical Japonica	504	68.50%	0.00%	12.30%	19.25%	NA
Japonica Intermediate	241	72.20%	8.70%	6.22%	12.86%	NA
VI/Aromatic	96	67.70%	0.00%	13.54%	18.75%	NA
Intermediate	90	55.60%	1.10%	8.89%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217187746	G -> DEL	N	N	silent_mutation	Average:5.84; most accessible tissue: Callus, score: 16.594	N	N	N	N
vg1217187746	G -> A	LOC_Os12g29030.1	downstream_gene_variant ; 1501.0bp to feature; MODIFIER	silent_mutation	Average:5.84; most accessible tissue: Callus, score: 16.594	N	N	N	N
vg1217187746	G -> A	LOC_Os12g29020-LOC_Os12g29030	intergenic_region ; MODIFIER	silent_mutation	Average:5.84; most accessible tissue: Callus, score: 16.594	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217187746	2.08E-06	2.08E-06	mr1412	Jap_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