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Detailed information for vg1217693047:

Variant ID: vg1217693047 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17693047
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, G: 0.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

GAGTAAGGATAAGCACCCTAATTGCAGGTACACGTTTGGGCCGGAAAAGTAGACGTTCCAGCACAGGTAATGAGAAAGCAGCTGTCTATAAAGAGTTCAA[T/G]
TAAGCTAAAGATAGATACTGATTCAAAATGCTCCCAAAGGGAAGTTTTTGTTAATTATATATACCTTCCCAGATCCTGTTATAGCACTGCCACATATATC

Reverse complement sequence

GATATATGTGGCAGTGCTATAACAGGATCTGGGAAGGTATATATAATTAACAAAAACTTCCCTTTGGGAGCATTTTGAATCAGTATCTATCTTTAGCTTA[A/C]
TTGAACTCTTTATAGACAGCTGCTTTCTCATTACCTGTGCTGGAACGTCTACTTTTCCGGCCCAAACGTGTACCTGCAATTAGGGTGCTTATCCTTACTC

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	88.20%	10.60%	0.08%	1.10%	NA
All Indica	2759	94.40%	3.80%	0.07%	1.74%	NA
All Japonica	1512	80.90%	18.70%	0.13%	0.26%	NA
Aus	269	69.90%	30.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	86.90%	9.00%	0.00%	4.16%	NA
Indica Intermediate	786	95.90%	2.50%	0.25%	1.27%	NA
Temperate Japonica	767	98.00%	2.00%	0.00%	0.00%	NA
Tropical Japonica	504	64.70%	35.10%	0.20%	0.00%	NA
Japonica Intermediate	241	60.20%	37.80%	0.41%	1.66%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	0.00%	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
vg1217693047	T -> DEL	N	N	silent_mutation	Average:46.747; most accessible tissue: Callus, score: 76.627	N	N	N	N
vg1217693047	T -> G	LOC_Os12g29670.1	upstream_gene_variant ; 1996.0bp to feature; MODIFIER	silent_mutation	Average:46.747; most accessible tissue: Callus, score: 76.627	N	N	N	N
vg1217693047	T -> G	LOC_Os12g29660.1	intron_variant ; MODIFIER	silent_mutation	Average:46.747; most accessible tissue: Callus, score: 76.627	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217693047	4.75E-06	NA	mr1748	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