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Detailed information for vg0911337326:

Variant ID: vg0911337326 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11337326
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTCACATTTCTTTAACGTTTCGTTCGCGTTCGTTAAGCGTTCGCTCGCATTCGTTCACGTTCGTTCGCGTTCGTTCGCGTTTGGTAACGTTCGTTTCG[C/T]
GTTCGTTAAGCGTTCGTTCGCGTTCGTTCGCGTTCGTTCACGTTCATTCACGTTCGTTCGAGTTCGTTCACTAACATTCACGTTCGTTCACGTTTCGGTC

Reverse complement sequence

GACCGAAACGTGAACGAACGTGAATGTTAGTGAACGAACTCGAACGAACGTGAATGAACGTGAACGAACGCGAACGAACGCGAACGAACGCTTAACGAAC[G/A]
CGAAACGAACGTTACCAAACGCGAACGAACGCGAACGAACGTGAACGAATGCGAGCGAACGCTTAACGAACGCGAACGAAACGTTAAAGAAATGTGAACG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.70%	8.00%	16.31%	37.94%	NA
All Indica	2759	22.70%	7.70%	23.38%	46.25%	NA
All Japonica	1512	72.00%	0.50%	3.24%	24.34%	NA
Aus	269	8.20%	31.20%	21.56%	39.03%	NA
Indica I	595	13.60%	2.70%	23.03%	60.67%	NA
Indica II	465	15.90%	3.00%	20.43%	60.65%	NA
Indica III	913	35.30%	14.70%	22.34%	27.71%	NA
Indica Intermediate	786	19.00%	6.10%	26.59%	48.35%	NA
Temperate Japonica	767	66.60%	0.10%	1.69%	31.55%	NA
Tropical Japonica	504	81.30%	0.00%	5.36%	13.29%	NA
Japonica Intermediate	241	69.30%	2.50%	3.73%	24.48%	NA
VI/Aromatic	96	9.40%	68.80%	7.29%	14.58%	NA
Intermediate	90	43.30%	10.00%	13.33%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911337326	C -> DEL	N	N	silent_mutation	Average:6.997; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg0911337326	C -> T	LOC_Os09g18490.1	upstream_gene_variant ; 989.0bp to feature; MODIFIER	silent_mutation	Average:6.997; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg0911337326	C -> T	LOC_Os09g18500.1	downstream_gene_variant ; 1489.0bp to feature; MODIFIER	silent_mutation	Average:6.997; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg0911337326	C -> T	LOC_Os09g18490-LOC_Os09g18500	intergenic_region ; MODIFIER	silent_mutation	Average:6.997; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911337326	4.03E-06	1.00E-06	mr1961	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