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Detailed information for vg0827543233:

Variant ID: vg0827543233 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27543233
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAATAAATACATAACCAAGCCAAAAATACATAACCACGTTCGCTGTGGAGGCTAGAAATTCCCGCATTAATCGGAGAAAAAGAAAAGAAGAGTCCAAATA[A/G]
AAATACAATAAAAAATAGCTGAAATTCGGAATAAAAAATATGCAATATTGAAAGAGAAGTCCATATAGGAACCCAATACGCGATTAATTAAAACTCGGAA

Reverse complement sequence

TTCCGAGTTTTAATTAATCGCGTATTGGGTTCCTATATGGACTTCTCTTTCAATATTGCATATTTTTTATTCCGAATTTCAGCTATTTTTTATTGTATTT[T/C]
TATTTGGACTCTTCTTTTCTTTTTCTCCGATTAATGCGGGAATTTCTAGCCTCCACAGCGAACGTGGTTATGTATTTTTGGCTTGGTTATGTATTTATTG

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	63.90%	36.10%	0.00%	0.00%	NA
All Indica	2759	97.70%	2.30%	0.00%	0.00%	NA
All Japonica	1512	2.60%	97.40%	0.00%	0.00%	NA
Aus	269	83.30%	16.70%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	97.40%	2.60%	0.00%	0.00%	NA
Indica III	913	97.60%	2.40%	0.00%	0.00%	NA
Indica Intermediate	786	96.60%	3.40%	0.00%	0.00%	NA
Temperate Japonica	767	2.30%	97.70%	0.00%	0.00%	NA
Tropical Japonica	504	2.80%	97.20%	0.00%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	7.30%	92.70%	0.00%	0.00%	NA
Intermediate	90	57.80%	42.20%	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
vg0827543233	A -> G	LOC_Os08g43550.1	downstream_gene_variant ; 4738.0bp to feature; MODIFIER	silent_mutation	Average:40.816; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0827543233	A -> G	LOC_Os08g43540-LOC_Os08g43550	intergenic_region ; MODIFIER	silent_mutation	Average:40.816; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827543233	4.89E-06	2.10E-06	mr1117	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