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Detailed information for vg0412908287:

Variant ID: vg0412908287 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12908287
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGTAGATAAATTTGTTGAAAAGAAAATTATGGATATGTGATCTTTTACTAATCATCATTGGGCATGTTTTCTTGAATTCGCAATAACCGATGCTCATTT[G/T]
GTTTGTCTGGAATGCATGTTTTGTTTTTCCTCACGGTCAAACCCATGAGCTATCAGAGTCCCAGTTCCATTGATTATAGAGAAATTAATGCTAGTAGTTC

Reverse complement sequence

GAACTACTAGCATTAATTTCTCTATAATCAATGGAACTGGGACTCTGATAGCTCATGGGTTTGACCGTGAGGAAAAACAAAACATGCATTCCAGACAAAC[C/A]
AAATGAGCATCGGTTATTGCGAATTCAAGAAAACATGCCCAATGATGATTAGTAAAAGATCACATATCCATAATTTTCTTTTCAACAAATTTATCTACCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.30%	44.30%	0.40%	0.00%	NA
All Indica	2759	83.30%	16.10%	0.62%	0.00%	NA
All Japonica	1512	1.90%	98.10%	0.00%	0.00%	NA
Aus	269	90.00%	9.70%	0.37%	0.00%	NA
Indica I	595	70.40%	28.70%	0.84%	0.00%	NA
Indica II	465	74.00%	25.20%	0.86%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	81.30%	17.70%	1.02%	0.00%	NA
Temperate Japonica	767	1.70%	98.30%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.90%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	38.90%	60.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412908287	G -> T	LOC_Os04g22790.1	upstream_gene_variant ; 2440.0bp to feature; MODIFIER	silent_mutation	Average:34.282; most accessible tissue: Callus, score: 83.417	N	N	N	N
vg0412908287	G -> T	LOC_Os04g22790-LOC_Os04g22800	intergenic_region ; MODIFIER	silent_mutation	Average:34.282; most accessible tissue: Callus, score: 83.417	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412908287	3.20E-06	NA	mr1583	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