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Detailed information for vg0816197134:

Variant ID: vg0816197134 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16197134
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGCTCGCGGAACATTGAAACCGCGACAGCTCGTTTTTGGAAAACATACCGATCGTCGCTACACTCGACTTATGCAAATACTTAAGCATTTCTGGATGCA[C/T]
ATGCCAAAAGTCGAGAGCGAATGATGAGGGCTGAAAAGTCAATGTGAATTCCTTTCGCTAACACGCAAGGGGGCCGACACGCCTCGCCCTTCTAAACGTA

Reverse complement sequence

TACGTTTAGAAGGGCGAGGCGTGTCGGCCCCCTTGCGTGTTAGCGAAAGGAATTCACATTGACTTTTCAGCCCTCATCATTCGCTCTCGACTTTTGGCAT[G/A]
TGCATCCAGAAATGCTTAAGTATTTGCATAAGTCGAGTGTAGCGACGATCGGTATGTTTTCCAAAAACGAGCTGTCGCGGTTTCAATGTTCCGCGAGCTG

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	31.10%	7.60%	21.94%	39.31%	NA
All Indica	2759	9.40%	12.70%	31.39%	46.50%	NA
All Japonica	1512	69.50%	0.30%	2.58%	27.65%	NA
Aus	269	9.30%	0.40%	42.01%	48.33%	NA
Indica I	595	17.00%	1.50%	9.24%	72.27%	NA
Indica II	465	7.70%	21.90%	22.37%	47.96%	NA
Indica III	913	4.70%	15.70%	50.49%	29.13%	NA
Indica Intermediate	786	10.10%	12.30%	31.30%	46.31%	NA
Temperate Japonica	767	98.00%	0.00%	0.13%	1.83%	NA
Tropical Japonica	504	25.40%	0.80%	6.94%	66.87%	NA
Japonica Intermediate	241	71.00%	0.00%	1.24%	27.80%	NA
VI/Aromatic	96	92.70%	0.00%	3.12%	4.17%	NA
Intermediate	90	52.20%	4.40%	17.78%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816197134	C -> T	LOC_Os08g26620.1	upstream_gene_variant ; 3573.0bp to feature; MODIFIER	silent_mutation	Average:10.108; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0816197134	C -> T	LOC_Os08g26650.1	upstream_gene_variant ; 3321.0bp to feature; MODIFIER	silent_mutation	Average:10.108; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0816197134	C -> T	LOC_Os08g26630.1	downstream_gene_variant ; 2138.0bp to feature; MODIFIER	silent_mutation	Average:10.108; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0816197134	C -> T	LOC_Os08g26630-LOC_Os08g26650	intergenic_region ; MODIFIER	silent_mutation	Average:10.108; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N
vg0816197134	C -> DEL	N	N	silent_mutation	Average:10.108; most accessible tissue: Minghui63 young leaf, score: 21.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816197134	4.62E-06	NA	mr1707	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
vg0816197134	3.29E-06	NA	mr1707	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