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Detailed information for vg0802984189:

Variant ID: vg0802984189 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2984189
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.84, G: 0.16, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

CAATAGAGTATTAATTGTCTCATCAATCAATTCTCATTCAAATTTTTTTCTATTCTACCCTTAACCACTCTTACCTATATTTCATTTAATGAGTGGCATC[G/A]
TAATCTTTTTTTAAAACCTTAATATATGATAGTAACCTAAAATTACAATTATTTTAGTATGGAGGTAGTATTTATTTTTTTCTTTGAGAAACACAGTACA

Reverse complement sequence

TGTACTGTGTTTCTCAAAGAAAAAAATAAATACTACCTCCATACTAAAATAATTGTAATTTTAGGTTACTATCATATATTAAGGTTTTAAAAAAAGATTA[C/T]
GATGCCACTCATTAAATGAAATATAGGTAAGAGTGGTTAAGGGTAGAATAGAAAAAAATTTGAATGAGAATTGATTGATGAGACAATTAATACTCTATTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.40%	32.20%	0.34%	0.00%	NA
All Indica	2759	59.30%	40.30%	0.40%	0.00%	NA
All Japonica	1512	92.60%	7.20%	0.20%	0.00%	NA
Aus	269	0.00%	100.00%	0.00%	0.00%	NA
Indica I	595	53.90%	45.70%	0.34%	0.00%	NA
Indica II	465	75.10%	24.50%	0.43%	0.00%	NA
Indica III	913	51.80%	48.10%	0.11%	0.00%	NA
Indica Intermediate	786	62.60%	36.60%	0.76%	0.00%	NA
Temperate Japonica	767	87.60%	12.10%	0.26%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.20%	0.00%	NA
Japonica Intermediate	241	95.40%	4.60%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	78.90%	18.90%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0802984189	G -> A	LOC_Os08g05570.3	downstream_gene_variant ; 1489.0bp to feature; MODIFIER	silent_mutation	Average:63.667; most accessible tissue: Callus, score: 80.686	N	N	N	N
vg0802984189	G -> A	LOC_Os08g05570.4	downstream_gene_variant ; 1489.0bp to feature; MODIFIER	silent_mutation	Average:63.667; most accessible tissue: Callus, score: 80.686	N	N	N	N
vg0802984189	G -> A	LOC_Os08g05580.1	intron_variant ; MODIFIER	silent_mutation	Average:63.667; most accessible tissue: Callus, score: 80.686	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802984189	NA	4.17E-06	mr1550_2	Jap_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
vg0802984189	NA	2.18E-06	mr1565_2	Jap_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
vg0802984189	4.28E-06	NA	mr1566_2	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
vg0802984189	NA	7.39E-06	mr1757_2	Jap_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