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Detailed information for vg0816652219:

Variant ID: vg0816652219 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16652219
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

ATCAGAACATAATTTTGTCTTCATGCTGAGTTGACTAACTATGGAAGCATCTGGTTCAGGAATATGCACTGATGAAGTCAGATCCACCAGTCACTCAGCG[C/T]
CGGTCTCCTCGCCAACACACTGCTCAGGGAGGTGGAGGGCCAACGATCAGACCGGATCCGCAACCTCAGACCTCCAAATCAACTGGTCAGACGGGTCCTC

Reverse complement sequence

GAGGACCCGTCTGACCAGTTGATTTGGAGGTCTGAGGTTGCGGATCCGGTCTGATCGTTGGCCCTCCACCTCCCTGAGCAGTGTGTTGGCGAGGAGACCG[G/A]
CGCTGAGTGACTGGTGGATCTGACTTCATCAGTGCATATTCCTGAACCAGATGCTTCCATAGTTAGTCAACTCAGCATGAAGACAAAATTATGTTCTGAT

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	50.50%	9.70%	34.64%	5.21%	NA
All Indica	2759	26.40%	15.40%	51.50%	6.67%	NA
All Japonica	1512	90.00%	0.40%	5.82%	3.77%	NA
Aus	269	78.40%	3.30%	18.22%	0.00%	NA
Indica I	595	27.10%	6.10%	62.35%	4.54%	NA
Indica II	465	37.20%	6.20%	50.32%	6.24%	NA
Indica III	913	17.50%	29.40%	45.45%	7.67%	NA
Indica Intermediate	786	29.90%	11.70%	51.02%	7.38%	NA
Temperate Japonica	767	91.70%	0.00%	2.09%	6.26%	NA
Tropical Japonica	504	88.50%	1.00%	10.52%	0.00%	NA
Japonica Intermediate	241	88.00%	0.40%	7.88%	3.73%	NA
VI/Aromatic	96	30.20%	14.60%	55.21%	0.00%	NA
Intermediate	90	61.10%	4.40%	28.89%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816652219	C -> T	LOC_Os08g27270.1	synonymous_variant ; p.Arg309Arg; LOW	synonymous_codon	Average:43.272; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0816652219	C -> DEL	LOC_Os08g27270.1	N	frameshift_variant	Average:43.272; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816652219	4.17E-06	NA	mr1004	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
vg0816652219	1.79E-06	NA	mr1005	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
vg0816652219	6.60E-07	6.16E-07	mr1011	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
vg0816652219	6.47E-06	6.45E-06	mr1012	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