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Detailed information for vg0608650180:

Variant ID: vg0608650180 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8650180
Reference Allele: G	Alternative Allele: C,T
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAGTAGCATTTATAAATCATAAGTTGAAAGCAGTAAAACAGTAGATAATTAAGTAGTATTAACATCATCACTGTCCAACGCTAAATCACGTTGCGACA[G/C,T]
GCCCAACCCAAAACCACCTGAACTACACCAGTTCATTAAGTCAAATTATTAAGGTGAGACTAATCACGGTGAGCTGGTTGACTGCCCAATAACCGTGGGC

Reverse complement sequence

GCCCACGGTTATTGGGCAGTCAACCAGCTCACCGTGATTAGTCTCACCTTAATAATTTGACTTAATGAACTGGTGTAGTTCAGGTGGTTTTGGGTTGGGC[C/G,A]
TGTCGCAACGTGATTTAGCGTTGGACAGTGATGATGTTAATACTACTTAATTATCTACTGTTTTACTGCTTTCAACTTATGATTTATAAATGCTACTTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.90%	18.20%	12.91%	32.92%	T: 0.02%
All Indica	2759	4.10%	19.90%	21.38%	54.58%	NA
All Japonica	1512	80.10%	18.90%	0.13%	0.86%	NA
Aus	269	85.50%	4.80%	3.35%	6.32%	NA
Indica I	595	2.00%	13.90%	17.82%	66.22%	NA
Indica II	465	4.10%	16.60%	21.72%	57.63%	NA
Indica III	913	3.90%	29.20%	21.80%	45.02%	NA
Indica Intermediate	786	6.00%	15.50%	23.41%	55.09%	NA
Temperate Japonica	767	63.10%	35.90%	0.26%	0.78%	NA
Tropical Japonica	504	98.20%	1.00%	0.00%	0.79%	NA
Japonica Intermediate	241	96.30%	2.50%	0.00%	1.24%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	0.00%	T: 1.04%
Intermediate	90	54.40%	13.30%	10.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608650180	G -> C	LOC_Os06g15250.1	upstream_gene_variant ; 3375.0bp to feature; MODIFIER	silent_mutation	Average:19.58; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0608650180	G -> C	LOC_Os06g15250-LOC_Os06g15260	intergenic_region ; MODIFIER	silent_mutation	Average:19.58; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0608650180	G -> T	LOC_Os06g15250.1	upstream_gene_variant ; 3375.0bp to feature; MODIFIER	silent_mutation	Average:19.58; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0608650180	G -> T	LOC_Os06g15250-LOC_Os06g15260	intergenic_region ; MODIFIER	silent_mutation	Average:19.58; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0608650180	G -> DEL	N	N	silent_mutation	Average:19.58; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608650180	NA	4.39E-09	mr1047	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
vg0608650180	6.39E-06	6.39E-06	mr1296	Ind_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
vg0608650180	4.04E-06	1.30E-07	mr1518	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
vg0608650180	NA	5.63E-18	mr1552	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
vg0608650180	NA	9.71E-09	mr1648	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
vg0608650180	NA	6.57E-13	mr1655	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
vg0608650180	NA	8.62E-07	mr1748	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