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Detailed information for vg1009638506:

Variant ID: vg1009638506 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9638506
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, T: 0.35, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGAGGAGCCAATGAATGGGATTAGGGATTTGCCAGCCATTAGTGGGTATGAGTGGAAATTCGAGGAATTGGGTTGAATTGGAGAGGGGAGTGTGCAAA[T/G]
GTGGAGGAAAGGAGGAAGAAGAAGTGTTCTGGTGTGATCCGAACGTTCTACCTCCACACGCGCATCTAAACAGACTAGGGACGAGCGGGGGAGACTAGCA

Reverse complement sequence

TGCTAGTCTCCCCCGCTCGTCCCTAGTCTGTTTAGATGCGCGTGTGGAGGTAGAACGTTCGGATCACACCAGAACACTTCTTCTTCCTCCTTTCCTCCAC[A/C]
TTTGCACACTCCCCTCTCCAATTCAACCCAATTCCTCGAATTTCCACTCATACCCACTAATGGCTGGCAAATCCCTAATCCCATTCATTGGCTCCTCCTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.60%	25.20%	0.97%	31.23%	NA
All Indica	2759	56.80%	5.60%	1.38%	36.21%	NA
All Japonica	1512	24.10%	46.00%	0.40%	29.50%	NA
Aus	269	11.90%	86.20%	0.37%	1.49%	NA
Indica I	595	72.90%	3.00%	0.67%	23.36%	NA
Indica II	465	40.40%	3.70%	1.94%	53.98%	NA
Indica III	913	61.20%	4.30%	0.88%	33.63%	NA
Indica Intermediate	786	49.20%	10.20%	2.16%	38.42%	NA
Temperate Japonica	767	17.20%	55.80%	0.39%	26.60%	NA
Tropical Japonica	504	22.60%	33.50%	0.60%	43.25%	NA
Japonica Intermediate	241	49.00%	41.10%	0.00%	9.96%	NA
VI/Aromatic	96	19.80%	78.10%	1.04%	1.04%	NA
Intermediate	90	34.40%	36.70%	0.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009638506	T -> G	LOC_Os10g18930.1	upstream_gene_variant ; 60.0bp to feature; MODIFIER	silent_mutation	Average:68.424; most accessible tissue: Zhenshan97 young leaf, score: 82.982	N	N	N	N
vg1009638506	T -> G	LOC_Os10g18930-LOC_Os10g18940	intergenic_region ; MODIFIER	silent_mutation	Average:68.424; most accessible tissue: Zhenshan97 young leaf, score: 82.982	N	N	N	N
vg1009638506	T -> DEL	N	N	silent_mutation	Average:68.424; most accessible tissue: Zhenshan97 young leaf, score: 82.982	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009638506	NA	6.45E-06	mr1772	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
vg1009638506	1.18E-06	1.18E-06	mr1811	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