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Detailed information for vg0817684844:

Variant ID: vg0817684844 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17684844
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

AAATACTTACAGAAGAATAACTTAGTCCTCACCACGAAGAAAATTGCAGCGGAAAAATAAAATCTAGCGAAGCTTCAACTCAAATAGGATTTAAGACAAA[G/T]
GTTTTCTCCTTCTGAATCCTTTGTCTCCAAGTGAGGTTTGATGATTATTGCAAGGCGAGTATATGAAATACTTCACAAAGCACACAACAAGTATGCAAGT

Reverse complement sequence

ACTTGCATACTTGTTGTGTGCTTTGTGAAGTATTTCATATACTCGCCTTGCAATAATCATCAAACCTCACTTGGAGACAAAGGATTCAGAAGGAGAAAAC[C/A]
TTTGTCTTAAATCCTATTTGAGTTGAAGCTTCGCTAGATTTTATTTTTCCGCTGCAATTTTCTTCGTGGTGAGGACTAAGTTATTCTTCTGTAAGTATTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.00%	6.90%	0.11%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	84.50%	15.30%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	85.90%	13.80%	0.26%	0.00%	NA
Tropical Japonica	504	92.30%	7.70%	0.00%	0.00%	NA
Japonica Intermediate	241	63.50%	36.10%	0.41%	0.00%	NA
VI/Aromatic	96	19.80%	79.20%	1.04%	0.00%	NA
Intermediate	90	83.30%	15.60%	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
vg0817684844	G -> T	LOC_Os08g28930.1	upstream_gene_variant ; 2331.0bp to feature; MODIFIER	silent_mutation	Average:36.276; most accessible tissue: Zhenshan97 young leaf, score: 46.636	N	N	N	N
vg0817684844	G -> T	LOC_Os08g28920.1	intron_variant ; MODIFIER	silent_mutation	Average:36.276; most accessible tissue: Zhenshan97 young leaf, score: 46.636	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817684844	1.90E-06	1.91E-06	mr1894	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