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Detailed information for vg1213936119:

Variant ID: vg1213936119 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13936119
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:

GAATGACCCAATGGTAAGCATGTTTATTCGCAAATTTATGGGCTATATATATCCAGTTATTCTTCATAAATGGGGAAATGATTTACATCAAAAGAAAATA[A/G]
TTAGTGAGAAAATGAAGTTAGGGAGAAAATAATTAGTGGCAAGGTTTAGAACCAGGCAGAGGTGCAGCCCACCTCCTGCCGACTATATCATACGCGATGT

Reverse complement sequence

ACATCGCGTATGATATAGTCGGCAGGAGGTGGGCTGCACCTCTGCCTGGTTCTAAACCTTGCCACTAATTATTTTCTCCCTAACTTCATTTTCTCACTAA[T/C]
TATTTTCTTTTGATGTAAATCATTTCCCCATTTATGAAGAATAACTGGATATATATAGCCCATAAATTTGCGAATAAACATGCTTACCATTGGGTCATTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.00%	13.30%	0.63%	0.00%	NA
All Indica	2759	97.10%	2.00%	0.87%	0.00%	NA
All Japonica	1512	66.50%	33.20%	0.33%	0.00%	NA
Aus	269	83.30%	16.70%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	90.30%	6.00%	3.66%	0.00%	NA
Indica III	913	98.00%	1.60%	0.33%	0.00%	NA
Indica Intermediate	786	98.00%	1.50%	0.51%	0.00%	NA
Temperate Japonica	767	89.20%	10.80%	0.00%	0.00%	NA
Tropical Japonica	504	31.90%	67.50%	0.60%	0.00%	NA
Japonica Intermediate	241	66.40%	32.80%	0.83%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	83.30%	15.60%	1.11%	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
vg1213936119	A -> G	LOC_Os12g24410.1	upstream_gene_variant ; 3557.0bp to feature; MODIFIER	silent_mutation	Average:22.713; most accessible tissue: Minghui63 flag leaf, score: 33.603	N	N	N	N
vg1213936119	A -> G	LOC_Os12g24430.1	upstream_gene_variant ; 2676.0bp to feature; MODIFIER	silent_mutation	Average:22.713; most accessible tissue: Minghui63 flag leaf, score: 33.603	N	N	N	N
vg1213936119	A -> G	LOC_Os12g24420.1	downstream_gene_variant ; 422.0bp to feature; MODIFIER	silent_mutation	Average:22.713; most accessible tissue: Minghui63 flag leaf, score: 33.603	N	N	N	N
vg1213936119	A -> G	LOC_Os12g24410-LOC_Os12g24420	intergenic_region ; MODIFIER	silent_mutation	Average:22.713; most accessible tissue: Minghui63 flag leaf, score: 33.603	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213936119	1.77E-06	1.93E-06	mr1622	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
vg1213936119	NA	6.59E-06	mr1622	Jap_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