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Detailed information for vg0810610033:

Variant ID: vg0810610033 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10610033
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGTTTTTTTATTTGGAATTTATTTACGAAGTGATTTTGGAGATGATTGGATTTCACAGGTGAATCTACAAGATACTGATGTTATTTTATGTGGACCGG[T/G]
CAGACCAGCCAGTCCGCGGTCTGACCGGCCGACTCTGTGTCGGTTTCGGTTTCGGGTTATTTGTTTGGATATCCGTGATTATTTCATGAGTATGGCTTCT

Reverse complement sequence

AGAAGCCATACTCATGAAATAATCACGGATATCCAAACAAATAACCCGAAACCGAAACCGACACAGAGTCGGCCGGTCAGACCGCGGACTGGCTGGTCTG[A/C]
CCGGTCCACATAAAATAACATCAGTATCTTGTAGATTCACCTGTGAAATCCAATCATCTCCAAAATCACTTCGTAAATAAATTCCAAATAAAAAAACAAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.20%	0.60%	6.98%	1.25%	NA
All Indica	2759	86.00%	0.80%	11.13%	2.03%	NA
All Japonica	1512	98.80%	0.10%	0.99%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	88.90%	0.50%	9.92%	0.67%	NA
Indica II	465	67.50%	1.70%	23.87%	6.88%	NA
Indica III	913	96.50%	0.20%	3.07%	0.22%	NA
Indica Intermediate	786	82.60%	1.30%	13.87%	2.29%	NA
Temperate Japonica	767	98.40%	0.30%	1.30%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.40%	0.20%	NA
Japonica Intermediate	241	98.80%	0.00%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	1.10%	8.89%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0810610033	T -> G	LOC_Os08g17340.1	downstream_gene_variant ; 139.0bp to feature; MODIFIER	silent_mutation	Average:56.941; most accessible tissue: Minghui63 flag leaf, score: 78.154	N	N	N	N
vg0810610033	T -> G	LOC_Os08g17350.1	downstream_gene_variant ; 3059.0bp to feature; MODIFIER	silent_mutation	Average:56.941; most accessible tissue: Minghui63 flag leaf, score: 78.154	N	N	N	N
vg0810610033	T -> G	LOC_Os08g17360.1	downstream_gene_variant ; 4991.0bp to feature; MODIFIER	silent_mutation	Average:56.941; most accessible tissue: Minghui63 flag leaf, score: 78.154	N	N	N	N
vg0810610033	T -> G	LOC_Os08g17340-LOC_Os08g17350	intergenic_region ; MODIFIER	silent_mutation	Average:56.941; most accessible tissue: Minghui63 flag leaf, score: 78.154	N	N	N	N
vg0810610033	T -> DEL	N	N	silent_mutation	Average:56.941; most accessible tissue: Minghui63 flag leaf, score: 78.154	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810610033	1.20E-06	2.19E-07	mr1120	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