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Detailed information for vg0906782983:

Variant ID: vg0906782983 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6782983
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGTTAACAATGTTAGAACAAATTGTTTACACCCAAATTTGGCACCTCGGATTAAAATAGGAAAGATTGCCAAAATTTGGAAGTCTACCGATTTCCTCC[G/A]
AGTGGGCCGGTCTGACCGCCGTGTGTTGGGCGGTCAGACCGCCGGTTGAGGGCCGGTCAGACCGGCGGTGTGTGGCCGGTCTGACTAGCAGGTCCGAGTC

Reverse complement sequence

GACTCGGACCTGCTAGTCAGACCGGCCACACACCGCCGGTCTGACCGGCCCTCAACCGGCGGTCTGACCGCCCAACACACGGCGGTCAGACCGGCCCACT[C/T]
GGAGGAAATCGGTAGACTTCCAAATTTTGGCAATCTTTCCTATTTTAATCCGAGGTGCCAAATTTGGGTGTAAACAATTTGTTCTAACATTGTTAACACT

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	89.80%	5.10%	5.04%	0.00%	NA
All Indica	2759	98.80%	0.60%	0.58%	0.00%	NA
All Japonica	1512	71.10%	14.60%	14.29%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.70%	1.90%	2.37%	0.00%	NA
Indica III	913	99.70%	0.20%	0.11%	0.00%	NA
Indica Intermediate	786	98.90%	0.60%	0.51%	0.00%	NA
Temperate Japonica	767	91.80%	5.60%	2.61%	0.00%	NA
Tropical Japonica	504	33.90%	31.00%	35.12%	0.00%	NA
Japonica Intermediate	241	83.00%	9.10%	7.88%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	91.10%	2.20%	6.67%	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
vg0906782983	G -> A	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	silent_mutation	Average:52.436; most accessible tissue: Zhenshan97 flower, score: 70.434	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906782983	9.49E-08	2.09E-16	mr1871	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
vg0906782983	NA	1.62E-08	mr1871	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
vg0906782983	NA	1.13E-09	mr1705_2	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
vg0906782983	4.25E-06	2.67E-14	mr1742_2	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
vg0906782983	4.57E-07	6.05E-20	mr1871_2	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