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Detailed information for vg0112570788:

Variant ID: vg0112570788 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12570788
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.69, A: 0.31, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TGTAGCCTTTCCAATTCTCGTCTCCTCCATCTTCTTCCCAAGACCATCTTCTCATCTTCCCTAGATATGTATTGTTGCGTTCTCCACCTATAGCTCCTAC[A/G]
ACCCGCTCCACACTAGATCCAAATTAAAAGCTCGAGCAGGCCGCACCAGCCAGATCTGCCCCTACCAAGAGGGGGGATGGGTGACGCCATCATCACCCGC

Reverse complement sequence

GCGGGTGATGATGGCGTCACCCATCCCCCCTCTTGGTAGGGGCAGATCTGGCTGGTGCGGCCTGCTCGAGCTTTTAATTTGGATCTAGTGTGGAGCGGGT[T/C]
GTAGGAGCTATAGGTGGAGAACGCAACAATACATATCTAGGGAAGATGAGAAGATGGTCTTGGGAAGAAGATGGAGGAGACGAGAATTGGAAAGGCTACA

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	59.00%	40.80%	0.21%	0.00%	NA
All Indica	2759	87.30%	12.40%	0.25%	0.00%	NA
All Japonica	1512	2.80%	97.10%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	92.00%	7.70%	0.22%	0.00%	NA
Indica III	913	78.50%	21.00%	0.44%	0.00%	NA
Indica Intermediate	786	85.80%	14.00%	0.25%	0.00%	NA
Temperate Japonica	767	0.70%	99.20%	0.13%	0.00%	NA
Tropical Japonica	504	6.50%	93.50%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	32.30%	67.70%	0.00%	0.00%	NA
Intermediate	90	43.30%	54.40%	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
vg0112570788	A -> G	LOC_Os01g22352.1	downstream_gene_variant ; 756.0bp to feature; MODIFIER	silent_mutation	Average:58.541; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0112570788	A -> G	LOC_Os01g22352-LOC_Os01g22370	intergenic_region ; MODIFIER	silent_mutation	Average:58.541; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112570788	NA	1.33E-21	mr1168	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
vg0112570788	4.67E-06	NA	mr1672	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
vg0112570788	NA	6.35E-08	mr1335_2	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