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Detailed information for vg0527368492:

Variant ID: vg0527368492 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 27368492
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCTACCCCAAATATTGTACTGGTGTGATTATCATGAATAAGAGCAATACCGGCTTCGCCCAACAGGATGTAGGGTTATTACCTGACAACTCAGGGGCCC[A/G]
AACCTGTATAAAAATCTCTGTATCCATGTCTTTTACCTCAGTCTCGCGTATATCCTAGCACCAATAATCCCCATACCATGCAAATACCAGAATTACGACA

Reverse complement sequence

TGTCGTAATTCTGGTATTTGCATGGTATGGGGATTATTGGTGCTAGGATATACGCGAGACTGAGGTAAAAGACATGGATACAGAGATTTTTATACAGGTT[T/C]
GGGCCCCTGAGTTGTCAGGTAATAACCCTACATCCTGTTGGGCGAAGCCGGTATTGCTCTTATTCATGATAATCACACCAGTACAATATTTGGGGTAGCC

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	88.10%	11.80%	0.11%	0.00%	NA
All Indica	2759	87.40%	12.50%	0.04%	0.00%	NA
All Japonica	1512	88.60%	11.40%	0.00%	0.00%	NA
Aus	269	98.10%	0.40%	1.49%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	93.50%	6.20%	0.22%	0.00%	NA
Indica III	913	77.10%	22.90%	0.00%	0.00%	NA
Indica Intermediate	786	86.40%	13.60%	0.00%	0.00%	NA
Temperate Japonica	767	80.80%	19.20%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	91.30%	8.70%	0.00%	0.00%	NA
VI/Aromatic	96	79.20%	20.80%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	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
vg0527368492	A -> G	LOC_Os05g47770.1	downstream_gene_variant ; 947.0bp to feature; MODIFIER	silent_mutation	Average:68.424; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N
vg0527368492	A -> G	LOC_Os05g47770-LOC_Os05g47780	intergenic_region ; MODIFIER	silent_mutation	Average:68.424; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0527368492	2.69E-06	2.76E-06	mr1471_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