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Detailed information for vg0801862911:

Variant ID: vg0801862911 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1862911
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

AGGTATGTGGGCGGTCAGACCGGCAGGGTCCGAGTCCGAGTCTGTTTTCGTCGGGTCTCGGGTTTCCTTGCTCGGGAAGGCATGTTTCGTGTTTCCTTTG[G/A]
TTTCTATCCCGAGTTGGACGTAGAGAAGGGCCTATAGAGGGTAAGACCAACCCCTATTTAAGGGACAAGGCCGGTTCATTGTAAAACCCCCAAATACAAT

Reverse complement sequence

ATTGTATTTGGGGGTTTTACAATGAACCGGCCTTGTCCCTTAAATAGGGGTTGGTCTTACCCTCTATAGGCCCTTCTCTACGTCCAACTCGGGATAGAAA[C/T]
CAAAGGAAACACGAAACATGCCTTCCCGAGCAAGGAAACCCGAGACCCGACGAAAACAGACTCGGACTCGGACCCTGCCGGTCTGACCGCCCACATACCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.00%	11.60%	1.08%	3.28%	NA
All Indica	2759	73.30%	19.40%	1.81%	5.51%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.07%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	96.50%	3.40%	0.00%	0.17%	NA
Indica II	465	91.20%	5.60%	0.65%	2.58%	NA
Indica III	913	41.50%	42.20%	3.83%	12.49%	NA
Indica Intermediate	786	81.90%	13.40%	1.53%	3.18%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801862911	G -> A	LOC_Os08g03910.1	upstream_gene_variant ; 526.0bp to feature; MODIFIER	silent_mutation	Average:53.383; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0801862911	G -> A	LOC_Os08g03920.1	upstream_gene_variant ; 3190.0bp to feature; MODIFIER	silent_mutation	Average:53.383; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0801862911	G -> A	LOC_Os08g03930.1	upstream_gene_variant ; 4899.0bp to feature; MODIFIER	silent_mutation	Average:53.383; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0801862911	G -> A	LOC_Os08g03900.1	downstream_gene_variant ; 3123.0bp to feature; MODIFIER	silent_mutation	Average:53.383; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0801862911	G -> A	LOC_Os08g03900-LOC_Os08g03910	intergenic_region ; MODIFIER	silent_mutation	Average:53.383; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0801862911	G -> DEL	N	N	silent_mutation	Average:53.383; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801862911	5.48E-07	5.48E-07	mr1584_2	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