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Detailed information for vg1208535416:

Variant ID: vg1208535416 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8535416
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGTGTACCACTGTACCTACAAGACACAATCCCACAACATGTCACCATGCGCCTCAGTACCACCACGGTACCTTGAAAAGGAACTGTGACAATACCCCTC[G/A]
CACAACACAACCCACCACAGTGCACCGTTCCTGGATCATAATCTCCCCCTCAAAACCAGAGGCAATGGACTCCCCAGCGACCCCCACGGACTTCTCGCCG

Reverse complement sequence

CGGCGAGAAGTCCGTGGGGGTCGCTGGGGAGTCCATTGCCTCTGGTTTTGAGGGGGAGATTATGATCCAGGAACGGTGCACTGTGGTGGGTTGTGTTGTG[C/T]
GAGGGGTATTGTCACAGTTCCTTTTCAAGGTACCGTGGTGGTACTGAGGCGCATGGTGACATGTTGTGGGATTGTGTCTTGTAGGTACAGTGGTACACCT

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	79.80%	0.30%	3.70%	16.14%	NA
All Indica	2759	68.50%	0.10%	5.94%	25.44%	NA
All Japonica	1512	95.90%	0.90%	0.60%	2.58%	NA
Aus	269	95.20%	0.00%	0.74%	4.09%	NA
Indica I	595	62.50%	0.00%	3.36%	34.12%	NA
Indica II	465	68.60%	0.20%	7.31%	23.87%	NA
Indica III	913	73.10%	0.00%	6.79%	20.15%	NA
Indica Intermediate	786	67.80%	0.10%	6.11%	25.95%	NA
Temperate Japonica	767	95.00%	0.10%	0.26%	4.56%	NA
Tropical Japonica	504	96.80%	1.60%	0.99%	0.60%	NA
Japonica Intermediate	241	96.70%	2.10%	0.83%	0.41%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	90.00%	0.00%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208535416	G -> DEL	N	N	silent_mutation	Average:15.759; most accessible tissue: Callus, score: 25.715	N	N	N	N
vg1208535416	G -> A	LOC_Os12g14910.1	upstream_gene_variant ; 3747.0bp to feature; MODIFIER	silent_mutation	Average:15.759; most accessible tissue: Callus, score: 25.715	N	N	N	N
vg1208535416	G -> A	LOC_Os12g14920.1	upstream_gene_variant ; 913.0bp to feature; MODIFIER	silent_mutation	Average:15.759; most accessible tissue: Callus, score: 25.715	N	N	N	N
vg1208535416	G -> A	LOC_Os12g14910-LOC_Os12g14920	intergenic_region ; MODIFIER	silent_mutation	Average:15.759; most accessible tissue: Callus, score: 25.715	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208535416	3.02E-06	3.02E-06	mr1349	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