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Detailed information for vg0817306917:

Variant ID: vg0817306917 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17306917
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

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:

AGCCGAAGATTTAGGCTCTTCGCCTAGAGGTCAGCAAAGCGGAGGCGAACACCGAACCCAAAGGAGGCGGCGGTGAAGCTTGGTGATGATGGAAGTGTTG[G/C]
GATACGCGTAGGCTACGATAGCATAAATCAAAATTTTCTATCGCGTAAACCAGGAACCATGCAAGTATTAGATCATAGATCGTTACCACTCGACGCGCTG

Reverse complement sequence

CAGCGCGTCGAGTGGTAACGATCTATGATCTAATACTTGCATGGTTCCTGGTTTACGCGATAGAAAATTTTGATTTATGCTATCGTAGCCTACGCGTATC[C/G]
CAACACTTCCATCATCACCAAGCTTCACCGCCGCCTCCTTTGGGTTCGGTGTTCGCCTCCGCTTTGCTGACCTCTAGGCGAAGAGCCTAAATCTTCGGCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.80%	13.80%	1.14%	0.21%	NA
All Indica	2759	96.40%	1.30%	1.85%	0.36%	NA
All Japonica	1512	66.10%	33.70%	0.20%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	96.50%	1.80%	1.51%	0.17%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	95.80%	0.30%	2.96%	0.88%	NA
Indica Intermediate	786	96.40%	1.50%	1.91%	0.13%	NA
Temperate Japonica	767	72.80%	27.00%	0.26%	0.00%	NA
Tropical Japonica	504	64.10%	35.90%	0.00%	0.00%	NA
Japonica Intermediate	241	49.40%	50.20%	0.41%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	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
vg0817306917	G -> C	LOC_Os08g28350.1	upstream_gene_variant ; 2952.0bp to feature; MODIFIER	silent_mutation	Average:53.216; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N
vg0817306917	G -> C	LOC_Os08g28370.1	upstream_gene_variant ; 1319.0bp to feature; MODIFIER	silent_mutation	Average:53.216; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N
vg0817306917	G -> C	LOC_Os08g28360.1	downstream_gene_variant ; 87.0bp to feature; MODIFIER	silent_mutation	Average:53.216; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N
vg0817306917	G -> C	LOC_Os08g28360-LOC_Os08g28370	intergenic_region ; MODIFIER	silent_mutation	Average:53.216; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N
vg0817306917	G -> DEL	N	N	silent_mutation	Average:53.216; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817306917	3.49E-06	NA	mr1080	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