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Detailed information for vg0314390708:

Variant ID: vg0314390708 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14390708
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTGCCAACCAGCACGCAAATCGAAAGGGAAGCATATAGTAGTAGCATGTGGGCTACGACTGTATTCGTTGTTGGGAGTTTGGATGTAAACTCTCCGTA[C/T]
GGAAAATAGAGTGGTCCATTAGCACGTGATTAATTAAGTATTAGCTATTTTTTTAAAAAAAATGGATCAATATGATTTTTTAAGCAACTTTTGTATATAA

Reverse complement sequence

TTATATACAAAAGTTGCTTAAAAAATCATATTGATCCATTTTTTTTAAAAAAATAGCTAATACTTAATTAATCACGTGCTAATGGACCACTCTATTTTCC[G/A]
TACGGAGAGTTTACATCCAAACTCCCAACAACGAATACAGTCGTAGCCCACATGCTACTACTATATGCTTCCCTTTCGATTTGCGTGCTGGTTGGCAAGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.50%	0.10%	0.87%	39.55%	NA
All Indica	2759	35.60%	0.20%	1.49%	62.74%	NA
All Japonica	1512	99.60%	0.00%	0.00%	0.40%	NA
Aus	269	64.30%	0.00%	0.00%	35.69%	NA
Indica I	595	50.40%	0.00%	0.67%	48.91%	NA
Indica II	465	44.70%	0.20%	2.80%	52.26%	NA
Indica III	913	26.10%	0.30%	0.55%	73.06%	NA
Indica Intermediate	786	29.90%	0.30%	2.42%	67.43%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	73.30%	0.00%	0.00%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0314390708	C -> T	LOC_Os03g25150.1	downstream_gene_variant ; 2897.0bp to feature; MODIFIER	silent_mutation	Average:52.104; most accessible tissue: Callus, score: 81.85	N	N	N	N
vg0314390708	C -> T	LOC_Os03g25170.1	downstream_gene_variant ; 2478.0bp to feature; MODIFIER	silent_mutation	Average:52.104; most accessible tissue: Callus, score: 81.85	N	N	N	N
vg0314390708	C -> T	LOC_Os03g25180.1	downstream_gene_variant ; 4198.0bp to feature; MODIFIER	silent_mutation	Average:52.104; most accessible tissue: Callus, score: 81.85	N	N	N	N
vg0314390708	C -> T	LOC_Os03g25150-LOC_Os03g25170	intergenic_region ; MODIFIER	silent_mutation	Average:52.104; most accessible tissue: Callus, score: 81.85	N	N	N	N
vg0314390708	C -> DEL	N	N	silent_mutation	Average:52.104; most accessible tissue: Callus, score: 81.85	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314390708	5.57E-10	NA	mr1542	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
vg0314390708	2.19E-08	1.44E-11	mr1542	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
vg0314390708	1.36E-10	NA	mr1542_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
vg0314390708	8.08E-10	1.04E-14	mr1542_2	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
vg0314390708	1.29E-07	NA	mr1587_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
vg0314390708	4.85E-06	1.03E-06	mr1587_2	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