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Detailed information for vg0506632181:

Variant ID: vg0506632181 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6632181
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

TATGGCTGCACATCGGTCCCAGGATCCCCAGCCGTACATTCATCCTGCAATGGTCAGCCCATCAGGCAATCGTAGCAGCTGCGCCTCAACGGGGCAGGTC[G/A]
GATCACAGAGTATGGACGCCATGCAAACCCAGGACGAAACCACCTGCCCCGTTGATGAGATCATGCAGCGGACACCATGTGAGCTGCATATTACCTTCAA

Reverse complement sequence

TTGAAGGTAATATGCAGCTCACATGGTGTCCGCTGCATGATCTCATCAACGGGGCAGGTGGTTTCGTCCTGGGTTTGCATGGCGTCCATACTCTGTGATC[C/T]
GACCTGCCCCGTTGAGGCGCAGCTGCTACGATTGCCTGATGGGCTGACCATTGCAGGATGAATGTACGGCTGGGGATCCTGGGACCGATGTGCAGCCATA

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	95.50%	3.90%	0.61%	0.00%	NA
All Indica	2759	92.40%	6.60%	1.01%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.80%	0.80%	0.34%	0.00%	NA
Indica II	465	95.70%	4.10%	0.22%	0.00%	NA
Indica III	913	91.00%	8.90%	0.11%	0.00%	NA
Indica Intermediate	786	87.20%	9.80%	3.05%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0506632181	G -> A	LOC_Os05g11680-LOC_Os05g11700	intergenic_region ; MODIFIER	silent_mutation	Average:55.999; most accessible tissue: Zhenshan97 flag leaf, score: 77.738	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506632181	2.41E-06	2.41E-06	mr1464	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
vg0506632181	7.69E-06	7.69E-06	mr1905	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