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Detailed information for vg0613194984:

Variant ID: vg0613194984 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13194984
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTATCTAACTGTTGTCGACTTAGTGGTATGAAATGTTGACTCGTAGTCGACAACAGGGTAGCCTTCCTTCTCGAATCCGCATCCGGCGAGATCAAAGACA[G/A]
CGCTATGTCTCTCCTGACAGTATCCGTAGACATCGTAGGGGACTAGCCATGCTTATCTCTGAAGTCGATATCCGGCGTCTTGTCTTGGCGCATGTTGGCT

Reverse complement sequence

AGCCAACATGCGCCAAGACAAGACGCCGGATATCGACTTCAGAGATAAGCATGGCTAGTCCCCTACGATGTCTACGGATACTGTCAGGAGAGACATAGCG[C/T]
TGTCTTTGATCTCGCCGGATGCGGATTCGAGAAGGAAGGCTACCCTGTTGTCGACTACGAGTCAACATTTCATACCACTAAGTCGACAACAGTTAGATAA

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	82.00%	18.00%	0.02%	0.00%	NA
All Indica	2759	82.50%	17.50%	0.04%	0.00%	NA
All Japonica	1512	87.40%	12.60%	0.00%	0.00%	NA
Aus	269	39.80%	60.20%	0.00%	0.00%	NA
Indica I	595	86.90%	13.10%	0.00%	0.00%	NA
Indica II	465	94.00%	6.00%	0.00%	0.00%	NA
Indica III	913	71.90%	28.00%	0.11%	0.00%	NA
Indica Intermediate	786	84.70%	15.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	66.70%	33.30%	0.00%	0.00%	NA
Japonica Intermediate	241	92.10%	7.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0613194984	G -> A	LOC_Os06g22680.1	upstream_gene_variant ; 745.0bp to feature; MODIFIER	silent_mutation	Average:59.837; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0613194984	G -> A	LOC_Os06g22690.1	downstream_gene_variant ; 1312.0bp to feature; MODIFIER	silent_mutation	Average:59.837; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0613194984	G -> A	LOC_Os06g22680-LOC_Os06g22690	intergenic_region ; MODIFIER	silent_mutation	Average:59.837; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613194984	1.90E-06	NA	mr1033	Jap_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