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Detailed information for vg0614104823:

Variant ID: vg0614104823 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14104823
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, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CAGGTTACAGTTGATCCGAGCGAAGAGGTTGATGGCTTGCCGAGGCTGGTCCTCCTTGAGGGAATGAACAGTAAGACTGCTCTTTTCGCTACAAGCTTCC[G/A]
TGCTTTTGCTATTTTGCTTTATTTGACTTTTGACATGACTCCCCCTTGCCTTTACAGTGCTAACCCTCGACCAAGCTGAAGCCGAAGCCCGCAAGATGAT

Reverse complement sequence

ATCATCTTGCGGGCTTCGGCTTCAGCTTGGTCGAGGGTTAGCACTGTAAAGGCAAGGGGGAGTCATGTCAAAAGTCAAATAAAGCAAAATAGCAAAAGCA[C/T]
GGAAGCTTGTAGCGAAAAGAGCAGTCTTACTGTTCATTCCCTCAAGGAGGACCAGCCTCGGCAAGCCATCAACCTCTTCGCTCGGATCAACTGTAACCTG

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	69.00%	11.10%	5.08%	14.79%	NA
All Indica	2759	50.90%	18.80%	8.16%	22.18%	NA
All Japonica	1512	99.00%	0.20%	0.00%	0.79%	NA
Aus	269	77.00%	0.00%	2.23%	20.82%	NA
Indica I	595	30.10%	11.40%	8.74%	49.75%	NA
Indica II	465	28.20%	44.50%	10.32%	16.99%	NA
Indica III	913	76.80%	7.80%	6.68%	8.76%	NA
Indica Intermediate	786	50.00%	21.90%	8.14%	19.97%	NA
Temperate Japonica	767	98.70%	0.30%	0.00%	1.04%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	89.60%	2.10%	5.21%	3.12%	NA
Intermediate	90	75.60%	2.20%	4.44%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0614104823	G -> A	LOC_Os06g24090.1	upstream_gene_variant ; 3811.0bp to feature; MODIFIER	silent_mutation	Average:43.139; most accessible tissue: Minghui63 young leaf, score: 81.5	N	N	N	N
vg0614104823	G -> A	LOC_Os06g24110.1	downstream_gene_variant ; 2408.0bp to feature; MODIFIER	silent_mutation	Average:43.139; most accessible tissue: Minghui63 young leaf, score: 81.5	N	N	N	N
vg0614104823	G -> A	LOC_Os06g24100.1	intron_variant ; MODIFIER	silent_mutation	Average:43.139; most accessible tissue: Minghui63 young leaf, score: 81.5	N	N	N	N
vg0614104823	G -> DEL	N	N	silent_mutation	Average:43.139; most accessible tissue: Minghui63 young leaf, score: 81.5	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614104823	2.65E-08	NA	mr1632_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
vg0614104823	3.84E-06	NA	mr1632_2	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