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Detailed information for vg0809153211:

Variant ID: vg0809153211 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9153211
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAGCATTTTGATTCCGGGTATTTTGTTGTTGTTTGTAGGGATGTCGACGTCGAGGATGTCTAGCAGAGCGGGCAGCCTGAATTGCCTGTAGTTGTTCCG[G/A]
CACTTGCGCTTGAGCCGTATGTGCCGCAAGACGACGTAGACCAGGATCTACCCGTGGAGACGGGCATGGTGACGACTCCTTTAGGTTGGTTCTTGTCGTT

Reverse complement sequence

AACGACAAGAACCAACCTAAAGGAGTCGTCACCATGCCCGTCTCCACGGGTAGATCCTGGTCTACGTCGTCTTGCGGCACATACGGCTCAAGCGCAAGTG[C/T]
CGGAACAACTACAGGCAATTCAGGCTGCCCGCTCTGCTAGACATCCTCGACGTCGACATCCCTACAAACAACAACAAAATACCCGGAATCAAAATGCTAA

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	27.20%	25.40%	5.46%	41.98%	NA
All Indica	2759	35.60%	22.40%	8.12%	33.85%	NA
All Japonica	1512	1.00%	36.10%	1.79%	61.11%	NA
Aus	269	96.30%	1.50%	0.37%	1.86%	NA
Indica I	595	35.80%	16.60%	7.06%	40.50%	NA
Indica II	465	37.00%	24.90%	9.25%	28.82%	NA
Indica III	913	34.00%	24.60%	9.42%	31.98%	NA
Indica Intermediate	786	36.60%	22.60%	6.74%	33.97%	NA
Temperate Japonica	767	0.30%	60.60%	1.69%	37.42%	NA
Tropical Japonica	504	1.40%	4.00%	2.38%	92.26%	NA
Japonica Intermediate	241	2.50%	25.30%	0.83%	71.37%	NA
VI/Aromatic	96	9.40%	5.20%	1.04%	84.38%	NA
Intermediate	90	21.10%	28.90%	5.56%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809153211	G -> A	LOC_Os08g15110.1	downstream_gene_variant ; 1582.0bp to feature; MODIFIER	silent_mutation	Average:52.377; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0809153211	G -> A	LOC_Os08g15120.1	downstream_gene_variant ; 3086.0bp to feature; MODIFIER	silent_mutation	Average:52.377; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0809153211	G -> A	LOC_Os08g15100.1	intron_variant ; MODIFIER	silent_mutation	Average:52.377; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N
vg0809153211	G -> DEL	N	N	silent_mutation	Average:52.377; most accessible tissue: Minghui63 young leaf, score: 71.254	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809153211	6.18E-06	6.17E-06	mr1645	Jap_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