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Detailed information for vg0800884996:

Variant ID: vg0800884996 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 884996
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGGGATAATCACTTATATCAGAAGCTATTCATATTAGCTACACTTGGTCTATATCACCTGGAAGATTTATTACTCGGGAGCATGTTACATGCGTCATC[C/T]
TTTAAAGGGTGTCGAAGGCATATTTTTTGGCCTAGGCCTAATATGTCTGCAGCCCATATTTTCAGGTGTGGCCTGTCACGTTCTTTTAGGGACTTAGGCA

Reverse complement sequence

TGCCTAAGTCCCTAAAAGAACGTGACAGGCCACACCTGAAAATATGGGCTGCAGACATATTAGGCCTAGGCCAAAAAATATGCCTTCGACACCCTTTAAA[G/A]
GATGACGCATGTAACATGCTCCCGAGTAATAAATCTTCCAGGTGATATAGACCAAGTGTAGCTAATATGAATAGCTTCTGATATAAGTGATTATCCCTTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.40%	8.50%	0.13%	0.00%	NA
All Indica	2759	85.60%	14.10%	0.22%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	65.70%	33.40%	0.84%	0.00%	NA
Indica II	465	93.10%	6.90%	0.00%	0.00%	NA
Indica III	913	92.60%	7.40%	0.00%	0.00%	NA
Indica Intermediate	786	88.30%	11.60%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0800884996	C -> T	LOC_Os08g02310.1	upstream_gene_variant ; 1712.0bp to feature; MODIFIER	silent_mutation	Average:27.484; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N
vg0800884996	C -> T	LOC_Os08g02320.1	upstream_gene_variant ; 3815.0bp to feature; MODIFIER	silent_mutation	Average:27.484; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N
vg0800884996	C -> T	LOC_Os08g02310-LOC_Os08g02320	intergenic_region ; MODIFIER	silent_mutation	Average:27.484; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0800884996	2.50E-06	2.86E-07	mr1789	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