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Detailed information for vg1219330982:

Variant ID: vg1219330982 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19330982
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: 0.15, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TACCTGTCATCCACCTTGCGCCATTCTCTCTAATAGACGAACGAATAGGCGTGCCTTCGCGTCCCTGAAGCCAAACTAGCCAAATCTTCACGACCCGACC[G/A]
TGCATCTCTTGCCATCACTTATCCCGGCACCTCCTGATGTCACAGCACTGCCCAGCTACCCCGTTCCATCCCTCTCTACCCGAGAATGGCGAGACAGAGA

Reverse complement sequence

TCTCTGTCTCGCCATTCTCGGGTAGAGAGGGATGGAACGGGGTAGCTGGGCAGTGCTGTGACATCAGGAGGTGCCGGGATAAGTGATGGCAAGAGATGCA[C/T]
GGTCGGGTCGTGAAGATTTGGCTAGTTTGGCTTCAGGGACGCGAAGGCACGCCTATTCGTTCGTCTATTAGAGAGAATGGCGCAAGGTGGATGACAGGTA

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	39.70%	35.10%	0.66%	24.48%	NA
All Indica	2759	7.10%	56.50%	0.98%	35.41%	NA
All Japonica	1512	96.60%	2.60%	0.13%	0.66%	NA
Aus	269	27.50%	16.70%	0.37%	55.39%	NA
Indica I	595	10.10%	53.60%	1.18%	35.13%	NA
Indica II	465	6.00%	26.90%	1.51%	65.59%	NA
Indica III	913	3.30%	72.30%	0.66%	23.77%	NA
Indica Intermediate	786	9.80%	58.00%	0.89%	31.30%	NA
Temperate Japonica	767	97.90%	1.60%	0.26%	0.26%	NA
Tropical Japonica	504	97.60%	1.80%	0.00%	0.60%	NA
Japonica Intermediate	241	90.50%	7.50%	0.00%	2.07%	NA
VI/Aromatic	96	85.40%	7.30%	0.00%	7.29%	NA
Intermediate	90	72.20%	11.10%	1.11%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219330982	G -> DEL	N	N	silent_mutation	Average:30.388; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1219330982	G -> A	LOC_Os12g32030.1	upstream_gene_variant ; 3139.0bp to feature; MODIFIER	silent_mutation	Average:30.388; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1219330982	G -> A	LOC_Os12g32040.1	downstream_gene_variant ; 1585.0bp to feature; MODIFIER	silent_mutation	Average:30.388; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1219330982	G -> A	LOC_Os12g32030-LOC_Os12g32040	intergenic_region ; MODIFIER	silent_mutation	Average:30.388; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219330982	3.50E-07	NA	mr1458	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
vg1219330982	NA	4.21E-13	mr1713	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