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Detailed information for vg1220166852:

Variant ID: vg1220166852 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20166852
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTGCATGATGGATCGTGGTTCAGTTCTGCTAAAAAGAAAATAAAGTTACCGAAGGCCGTCACTCGGAAGACTTACATTTACAATACGAGTGGCTTCTCC[G/A]
AGCGCTTTCTTCAGCTGGCACACTTCTTCATCTTCTTTTTGACGGTTTATGACTATGCCGGCGGCTTGTGAGTTCTCGTCCTACCATTTGATCAAGATAG

Reverse complement sequence

CTATCTTGATCAAATGGTAGGACGAGAACTCACAAGCCGCCGGCATAGTCATAAACCGTCAAAAAGAAGATGAAGAAGTGTGCCAGCTGAAGAAAGCGCT[C/T]
GGAGAAGCCACTCGTATTGTAAATGTAAGTCTTCCGAGTGACGGCCTTCGGTAACTTTATTTTCTTTTTAGCAGAACTGAACCACGATCCATCATGCAGA

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	34.00%	0.30%	33.22%	32.46%	NA
All Indica	2759	18.30%	0.50%	40.01%	41.21%	NA
All Japonica	1512	65.70%	0.00%	17.72%	16.53%	NA
Aus	269	20.40%	0.00%	39.03%	40.52%	NA
Indica I	595	9.20%	1.00%	34.62%	55.13%	NA
Indica II	465	19.60%	0.00%	28.39%	52.04%	NA
Indica III	913	23.90%	0.70%	51.81%	23.66%	NA
Indica Intermediate	786	17.80%	0.30%	37.28%	44.66%	NA
Temperate Japonica	767	93.10%	0.00%	1.43%	5.48%	NA
Tropical Japonica	504	25.80%	0.00%	42.26%	31.94%	NA
Japonica Intermediate	241	62.20%	0.00%	18.26%	19.50%	NA
VI/Aromatic	96	10.40%	0.00%	69.79%	19.79%	NA
Intermediate	90	50.00%	0.00%	28.89%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220166852	G -> DEL	N	N	silent_mutation	Average:9.652; most accessible tissue: Callus, score: 26.012	N	N	N	N
vg1220166852	G -> A	LOC_Os12g33330.1	downstream_gene_variant ; 1305.0bp to feature; MODIFIER	silent_mutation	Average:9.652; most accessible tissue: Callus, score: 26.012	N	N	N	N
vg1220166852	G -> A	LOC_Os12g33350.1	downstream_gene_variant ; 3380.0bp to feature; MODIFIER	silent_mutation	Average:9.652; most accessible tissue: Callus, score: 26.012	N	N	N	N
vg1220166852	G -> A	LOC_Os12g33340.1	intron_variant ; MODIFIER	silent_mutation	Average:9.652; most accessible tissue: Callus, score: 26.012	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220166852	4.04E-06	6.02E-07	mr1117	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