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Detailed information for vg0608564755:

Variant ID: vg0608564755 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8564755
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAGCTGACTCCTGGTGGCTTCGAGGGTCCCGAGATGACGGACTAGCCTCTCTAAGGTTGCCGTTTTAGCTTCGTTCCTAAGATGAATCCTCTGCAAGAC[A/G]
GTTTAATTAGCGCCTAGATTAAAAGGCAAACGAGACGGTTGAGGTCAGGCGCCAAAGAGTTTACATTTACAATGCGGGTGGCTTGGCTGAGCGCCTTTTT

Reverse complement sequence

AAAAAGGCGCTCAGCCAAGCCACCCGCATTGTAAATGTAAACTCTTTGGCGCCTGACCTCAACCGTCTCGTTTGCCTTTTAATCTAGGCGCTAATTAAAC[T/C]
GTCTTGCAGAGGATTCATCTTAGGAACGAAGCTAAAACGGCAACCTTAGAGAGGCTAGTCCGTCATCTCGGGACCCTCGAAGCCACCAGGAGTCAGCTGT

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	58.40%	0.60%	1.59%	39.40%	NA
All Indica	2759	31.50%	1.00%	2.50%	64.99%	NA
All Japonica	1512	99.30%	0.10%	0.07%	0.60%	NA
Aus	269	86.60%	0.00%	0.74%	12.64%	NA
Indica I	595	26.90%	0.50%	2.86%	69.75%	NA
Indica II	465	30.10%	2.60%	3.01%	64.30%	NA
Indica III	913	34.70%	0.70%	1.53%	63.09%	NA
Indica Intermediate	786	32.10%	0.90%	3.05%	63.99%	NA
Temperate Japonica	767	99.20%	0.00%	0.13%	0.65%	NA
Tropical Japonica	504	99.40%	0.20%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	67.80%	1.10%	2.22%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608564755	A -> G	LOC_Os06g15100.1	downstream_gene_variant ; 1902.0bp to feature; MODIFIER	silent_mutation	Average:6.787; most accessible tissue: Callus, score: 24.19	N	N	N	N
vg0608564755	A -> G	LOC_Os06g15110.1	intron_variant ; MODIFIER	silent_mutation	Average:6.787; most accessible tissue: Callus, score: 24.19	N	N	N	N
vg0608564755	A -> DEL	N	N	silent_mutation	Average:6.787; most accessible tissue: Callus, score: 24.19	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608564755	3.21E-07	NA	mr1051_2	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
vg0608564755	1.62E-06	3.31E-06	mr1051_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