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Detailed information for vg1221569648:

Variant ID: vg1221569648 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21569648
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, G: 0.32, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCTCTGTTTCTCGCATGTGAACCAGGGCAACAGCTATATTGTCAAGATAGCCATCAAGGATTTAGTCCCTGCTGAAGCCTGGTGGTAAATAGCATGCA[A/G]
CACCTGTAAGAGAGGAGCAGGTAGAGATGGGAACACATATAAATGCTCGAGGTGCATCACTAATGCAATTGAAACAAGGTACTCTTACCACCTACACACG

Reverse complement sequence

CGTGTGTAGGTGGTAAGAGTACCTTGTTTCAATTGCATTAGTGATGCACCTCGAGCATTTATATGTGTTCCCATCTCTACCTGCTCCTCTCTTACAGGTG[T/C]
TGCATGCTATTTACCACCAGGCTTCAGCAGGGACTAAATCCTTGATGGCTATCTTGACAATATAGCTGTTGCCCTGGTTCACATGCGAGAAACAGAGGAA

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	68.80%	28.60%	1.50%	1.08%	NA
All Indica	2759	57.10%	39.60%	2.21%	1.09%	NA
All Japonica	1512	99.10%	0.70%	0.13%	0.00%	NA
Aus	269	15.20%	83.60%	1.12%	0.00%	NA
Indica I	595	69.10%	26.70%	2.69%	1.51%	NA
Indica II	465	68.40%	26.70%	3.87%	1.08%	NA
Indica III	913	38.90%	59.10%	1.10%	0.88%	NA
Indica Intermediate	786	62.60%	34.20%	2.16%	1.02%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	0.80%	0.83%	0.00%	NA
VI/Aromatic	96	66.70%	10.40%	2.08%	20.83%	NA
Intermediate	90	81.10%	14.40%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221569648	A -> DEL	N	N	silent_mutation	Average:57.134; most accessible tissue: Minghui63 flag leaf, score: 83.412	N	N	N	N
vg1221569648	A -> G	LOC_Os12g35480.1	upstream_gene_variant ; 4483.0bp to feature; MODIFIER	silent_mutation	Average:57.134; most accessible tissue: Minghui63 flag leaf, score: 83.412	N	N	N	N
vg1221569648	A -> G	LOC_Os12g35460.1	downstream_gene_variant ; 1360.0bp to feature; MODIFIER	silent_mutation	Average:57.134; most accessible tissue: Minghui63 flag leaf, score: 83.412	N	N	N	N
vg1221569648	A -> G	LOC_Os12g35470.1	downstream_gene_variant ; 1813.0bp to feature; MODIFIER	silent_mutation	Average:57.134; most accessible tissue: Minghui63 flag leaf, score: 83.412	N	N	N	N
vg1221569648	A -> G	LOC_Os12g35465.1	intron_variant ; MODIFIER	silent_mutation	Average:57.134; most accessible tissue: Minghui63 flag leaf, score: 83.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221569648	6.50E-07	1.91E-06	mr1871_2	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