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Detailed information for vg1219947105:

Variant ID: vg1219947105 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19947105
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.01, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

GTTAGTGAACTAGGGTTTCTTGCGGCGGTGGAGAAGGCAAAGAGCGCTGGTAGGCGGTGTGTGTTCAACAGGGTTGGCGGACTTCAAAATGGGCTCCCAA[A/T]
ATTCCTTTAAATAGACACACTACCGACGGTGCGAATTATACTAATCTGGCTATAGAGGAGATTATTGGATTATACTAATCTGGCTATAGATTATAATAAT

Reverse complement sequence

ATTATTATAATCTATAGCCAGATTAGTATAATCCAATAATCTCCTCTATAGCCAGATTAGTATAATTCGCACCGTCGGTAGTGTGTCTATTTAAAGGAAT[T/A]
TTGGGAGCCCATTTTGAAGTCCGCCAACCCTGTTGAACACACACCGCCTACCAGCGCTCTTTGCCTTCTCCACCGCCGCAAGAAACCCTAGTTCACTAAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.70%	3.80%	0.76%	1.78%	NA
All Indica	2759	91.00%	5.10%	1.16%	2.68%	NA
All Japonica	1512	99.00%	0.90%	0.07%	0.00%	NA
Aus	269	88.50%	7.40%	0.37%	3.72%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	84.50%	12.00%	1.29%	2.15%	NA
Indica III	913	89.40%	5.30%	1.64%	3.72%	NA
Indica Intermediate	786	90.20%	4.60%	1.40%	3.82%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	2.22%	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
vg1219947105	A -> DEL	N	N	silent_mutation	Average:73.521; most accessible tissue: Minghui63 flag leaf, score: 83.197	N	N	N	N
vg1219947105	A -> T	LOC_Os12g33010.1	upstream_gene_variant ; 134.0bp to feature; MODIFIER	silent_mutation	Average:73.521; most accessible tissue: Minghui63 flag leaf, score: 83.197	N	N	N	N
vg1219947105	A -> T	LOC_Os12g33020.1	upstream_gene_variant ; 983.0bp to feature; MODIFIER	silent_mutation	Average:73.521; most accessible tissue: Minghui63 flag leaf, score: 83.197	N	N	N	N
vg1219947105	A -> T	LOC_Os12g33000.1	downstream_gene_variant ; 4098.0bp to feature; MODIFIER	silent_mutation	Average:73.521; most accessible tissue: Minghui63 flag leaf, score: 83.197	N	N	N	N
vg1219947105	A -> T	LOC_Os12g33010-LOC_Os12g33020	intergenic_region ; MODIFIER	silent_mutation	Average:73.521; most accessible tissue: Minghui63 flag leaf, score: 83.197	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219947105	NA	3.01E-06	mr1377	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
vg1219947105	1.08E-06	1.08E-06	mr1377	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