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Detailed information for vg0714854525:

Variant ID: vg0714854525 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14854525
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGCTAATTTATCCGAGTCTAGGTCATCCTCATATCTTTATTTTTATTTCTTCTTCTTTTATTTTTTTCCTTGTTGGAGCAACCAACAATTCAAAACAT[C/T]
TCTGCTCCTCGGGCTGATCTTTGTGAGCCATCGTGTTCTTCAAAACCAATACTTTCGAATGGCTACGAAATCAGTCCTGGCTTTATAGCCATGGTTCGAG

Reverse complement sequence

CTCGAACCATGGCTATAAAGCCAGGACTGATTTCGTAGCCATTCGAAAGTATTGGTTTTGAAGAACACGATGGCTCACAAAGATCAGCCCGAGGAGCAGA[G/A]
ATGTTTTGAATTGTTGGTTGCTCCAACAAGGAAAAAAATAAAAGAAGAAGAAATAAAAATAAAGATATGAGGATGACCTAGACTCGGATAAATTAGCAAC

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	45.70%	7.70%	0.63%	45.96%	NA
All Indica	2759	17.00%	12.10%	1.01%	69.95%	NA
All Japonica	1512	99.30%	0.00%	0.00%	0.66%	NA
Aus	269	18.60%	10.00%	0.74%	70.63%	NA
Indica I	595	25.20%	30.60%	1.34%	42.86%	NA
Indica II	465	20.00%	6.20%	1.08%	72.69%	NA
Indica III	913	3.00%	1.80%	0.99%	94.30%	NA
Indica Intermediate	786	25.20%	13.50%	0.76%	60.56%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	86.50%	0.00%	0.00%	13.54%	NA
Intermediate	90	61.10%	6.70%	0.00%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714854525	C -> DEL	N	N	silent_mutation	Average:12.885; most accessible tissue: Callus, score: 33.964	N	N	N	N
vg0714854525	C -> T	LOC_Os07g25860.1	upstream_gene_variant ; 91.0bp to feature; MODIFIER	silent_mutation	Average:12.885; most accessible tissue: Callus, score: 33.964	N	N	N	N
vg0714854525	C -> T	LOC_Os07g25870.1	upstream_gene_variant ; 3838.0bp to feature; MODIFIER	silent_mutation	Average:12.885; most accessible tissue: Callus, score: 33.964	N	N	N	N
vg0714854525	C -> T	LOC_Os07g25850-LOC_Os07g25860	intergenic_region ; MODIFIER	silent_mutation	Average:12.885; most accessible tissue: Callus, score: 33.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714854525	7.80E-06	1.72E-09	mr1575	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
vg0714854525	1.02E-06	1.02E-06	mr1575	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
vg0714854525	NA	3.30E-06	mr1198_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