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Detailed information for vg0817806978:

Variant ID: vg0817806978 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17806978
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

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

Flanking Sequence (100 bp) in Reference Genome:

TCTCACCGCCAACAGAACCACCACAGCCTACGAAGTCGGAGCCTACAGGAGCCAAGTTGCTGGGGTGATCTAGTCGAGCCAACTCGACTACGGTCTCGTC[A/G]
GTATCATCGATTTCTGCTATTCCCTTTGTAATCTGTGGCTTCCATTATATAATCCCATATCAACTGGATTAGGGCTATTACCTATTAAGGGGCCTGAACC

Reverse complement sequence

GGTTCAGGCCCCTTAATAGGTAATAGCCCTAATCCAGTTGATATGGGATTATATAATGGAAGCCACAGATTACAAAGGGAATAGCAGAAATCGATGATAC[T/C]
GACGAGACCGTAGTCGAGTTGGCTCGACTAGATCACCCCAGCAACTTGGCTCCTGTAGGCTCCGACTTCGTAGGCTGTGGTGGTTCTGTTGGCGGTGAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	18.60%	7.40%	0.76%	73.25%	NA
All Indica	2759	1.40%	3.80%	1.05%	93.73%	NA
All Japonica	1512	54.10%	0.10%	0.26%	45.50%	NA
Aus	269	0.40%	85.90%	0.37%	13.38%	NA
Indica I	595	2.90%	0.30%	2.52%	94.29%	NA
Indica II	465	1.10%	5.60%	0.22%	93.12%	NA
Indica III	913	0.50%	3.00%	0.11%	96.39%	NA
Indica Intermediate	786	1.70%	6.20%	1.53%	90.59%	NA
Temperate Japonica	767	82.30%	0.00%	0.26%	17.47%	NA
Tropical Japonica	504	21.00%	0.20%	0.40%	78.37%	NA
Japonica Intermediate	241	33.60%	0.40%	0.00%	65.98%	NA
VI/Aromatic	96	1.00%	4.20%	0.00%	94.79%	NA
Intermediate	90	18.90%	11.10%	2.22%	67.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817806978	A -> G	LOC_Os08g29080.1	upstream_gene_variant ; 768.0bp to feature; MODIFIER	silent_mutation	Average:17.187; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0817806978	A -> G	LOC_Os08g29080-LOC_Os08g29090	intergenic_region ; MODIFIER	silent_mutation	Average:17.187; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0817806978	A -> DEL	N	N	silent_mutation	Average:17.187; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817806978	4.82E-07	3.68E-07	mr1833	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