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Detailed information for vg0606533311:

Variant ID: vg0606533311 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 6533311
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGTTTTCGTATCCAACTTTGACTGTCCGTCTTATATGAAATTTTTTTATAATTCGTATTTTCATAGTTGTTATCATTATTGTTAGATGATAAAATATG[G/A]
TTAATATTTTATGCGTGACTTGTCTTTTTTATTTTTTTCGTAATTTTTTTAAATAAGACGAATGGTCAAACGTTGGACACGGAAACCAGGGTTTCTCTTT

Reverse complement sequence

AAAGAGAAACCCTGGTTTCCGTGTCCAACGTTTGACCATTCGTCTTATTTAAAAAAATTACGAAAAAAATAAAAAAGACAAGTCACGCATAAAATATTAA[C/T]
CATATTTTATCATCTAACAATAATGATAACAACTATGAAAATACGAATTATAAAAAAATTTCATATAAGACGGACAGTCAAAGTTGGATACGAAAACCCA

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	54.60%	32.80%	0.47%	12.17%	NA
All Indica	2759	38.30%	40.50%	0.65%	20.51%	NA
All Japonica	1512	96.00%	3.60%	0.13%	0.26%	NA
Aus	269	3.00%	96.70%	0.37%	0.00%	NA
Indica I	595	38.70%	8.10%	1.18%	52.10%	NA
Indica II	465	61.70%	32.30%	0.43%	5.59%	NA
Indica III	913	24.30%	72.60%	0.33%	2.74%	NA
Indica Intermediate	786	40.60%	32.60%	0.76%	26.08%	NA
Temperate Japonica	767	99.10%	0.40%	0.13%	0.39%	NA
Tropical Japonica	504	91.50%	8.30%	0.20%	0.00%	NA
Japonica Intermediate	241	95.40%	4.10%	0.00%	0.41%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	65.60%	27.80%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0606533311	G -> A	LOC_Os06g12190.1	upstream_gene_variant ; 1435.0bp to feature; MODIFIER	silent_mutation	Average:43.605; most accessible tissue: Callus, score: 72.582	N	N	N	N
vg0606533311	G -> A	LOC_Os06g12200.1	downstream_gene_variant ; 4638.0bp to feature; MODIFIER	silent_mutation	Average:43.605; most accessible tissue: Callus, score: 72.582	N	N	N	N
vg0606533311	G -> A	LOC_Os06g12180-LOC_Os06g12190	intergenic_region ; MODIFIER	silent_mutation	Average:43.605; most accessible tissue: Callus, score: 72.582	N	N	N	N
vg0606533311	G -> DEL	N	N	silent_mutation	Average:43.605; most accessible tissue: Callus, score: 72.582	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0606533311	NA	2.85E-06	mr1252	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0606533311	3.77E-06	7.09E-06	mr1377	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
vg0606533311	3.51E-06	3.50E-06	mr1377	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0606533311	NA	1.77E-06	mr1695	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251