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Detailed information for vg1222391001:

Variant ID: vg1222391001 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22391001
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.16, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

AGTAGGTGTCGGACAAGTTGTAGAGGGGTATAGTGGCATTGTTTGATAGGACTTCTAAAAATTATAAAAAATGAAATGCAAGTCCAATTTTTAAAAGTTC[G/A]
GAATTTCCAAAAAGTAAAAAAACCCAATGATAATCATGTTCGATTTTAAAATCTCAATGACAATAAAGAAGGGAGGCAGCGGGCGAGCCGTAGAGAAGTA

Reverse complement sequence

TACTTCTCTACGGCTCGCCCGCTGCCTCCCTTCTTTATTGTCATTGAGATTTTAAAATCGAACATGATTATCATTGGGTTTTTTTACTTTTTGGAAATTC[C/T]
GAACTTTTAAAAATTGGACTTGCATTTCATTTTTTATAATTTTTAGAAGTCCTATCAAACAATGCCACTATACCCCTCTACAACTTGTCCGACACCTACT

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	62.60%	17.90%	13.84%	5.65%	NA
All Indica	2759	48.90%	26.30%	15.59%	9.17%	NA
All Japonica	1512	89.80%	5.40%	4.17%	0.66%	NA
Aus	269	32.00%	10.40%	57.25%	0.37%	NA
Indica I	595	67.60%	16.80%	8.24%	7.39%	NA
Indica II	465	62.60%	17.60%	18.28%	1.51%	NA
Indica III	913	26.80%	39.10%	20.26%	13.80%	NA
Indica Intermediate	786	52.40%	23.80%	14.12%	9.67%	NA
Temperate Japonica	767	96.50%	0.80%	2.35%	0.39%	NA
Tropical Japonica	504	77.80%	13.90%	7.34%	0.99%	NA
Japonica Intermediate	241	93.80%	2.10%	3.32%	0.83%	NA
VI/Aromatic	96	93.80%	1.00%	4.17%	1.04%	NA
Intermediate	90	84.40%	10.00%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222391001	G -> DEL	N	N	silent_mutation	Average:25.579; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1222391001	G -> A	LOC_Os12g36560.1	upstream_gene_variant ; 2094.0bp to feature; MODIFIER	silent_mutation	Average:25.579; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1222391001	G -> A	LOC_Os12g36580.1	upstream_gene_variant ; 2303.0bp to feature; MODIFIER	silent_mutation	Average:25.579; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg1222391001	G -> A	LOC_Os12g36570.1	intron_variant ; MODIFIER	silent_mutation	Average:25.579; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222391001	NA	6.95E-06	mr1125	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