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Detailed information for vg0817790397:

Variant ID: vg0817790397 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17790397
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.87, G: 0.13, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATTAATAGATAGGATCGCCTTCCCAGGACTCTATCCATGCGTGGCGATCATCTTGAAGCACATCAACTTGAACCCGATGTCGTACACAAGTCGTTTT[T/G]
TCAGAATCGGCTGAATCACTTAACCCAGTCTGACTCGGATTTAGCCGATCCTAATCGTAGCCGATCCGGACTTCAGCCGATTCTTACTCTGTTTCTGCAA

Reverse complement sequence

TTGCAGAAACAGAGTAAGAATCGGCTGAAGTCCGGATCGGCTACGATTAGGATCGGCTAAATCCGAGTCAGACTGGGTTAAGTGATTCAGCCGATTCTGA[A/C]
AAAACGACTTGTGTACGACATCGGGTTCAAGTTGATGTGCTTCAAGATGATCGCCACGCATGGATAGAGTCCTGGGAAGGCGATCCTATCTATTAATTAG

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	32.30%	17.80%	6.22%	43.69%	NA
All Indica	2759	20.70%	20.30%	9.57%	49.51%	NA
All Japonica	1512	60.90%	1.70%	0.86%	36.51%	NA
Aus	269	3.00%	87.00%	1.12%	8.92%	NA
Indica I	595	36.50%	20.50%	23.36%	19.66%	NA
Indica II	465	26.70%	8.00%	4.30%	61.08%	NA
Indica III	913	2.10%	31.20%	4.27%	62.43%	NA
Indica Intermediate	786	26.70%	14.60%	8.40%	50.25%	NA
Temperate Japonica	767	83.70%	0.30%	0.65%	15.38%	NA
Tropical Japonica	504	35.10%	4.20%	0.99%	59.72%	NA
Japonica Intermediate	241	42.30%	1.20%	1.24%	55.19%	NA
VI/Aromatic	96	1.00%	7.30%	6.25%	85.42%	NA
Intermediate	90	30.00%	15.60%	8.89%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817790397	T -> G	LOC_Os08g29050.1	upstream_gene_variant ; 3130.0bp to feature; MODIFIER	silent_mutation	Average:6.995; most accessible tissue: Callus, score: 21.555	N	N	N	N
vg0817790397	T -> G	LOC_Os08g29040-LOC_Os08g29050	intergenic_region ; MODIFIER	silent_mutation	Average:6.995; most accessible tissue: Callus, score: 21.555	N	N	N	N
vg0817790397	T -> DEL	N	N	silent_mutation	Average:6.995; most accessible tissue: Callus, score: 21.555	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817790397	NA	3.73E-07	mr1250_2	Jap_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
vg0817790397	2.47E-06	2.47E-06	mr1440_2	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