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Detailed information for vg0713647333:

Variant ID: vg0713647333 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13647333
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: 81. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCTAGGACCAGCACGGTGCTTGACTTTGAACAATTATTCAACTTTGCATTCTCTGATTTGAGCATTTGTTATTCCTTTGCTACATATTAAAGCCTACC[C/T]
AGAGCTCCACAGATTTGATTGCAGCCATACAGCAAGTGTTCGCCAAGGCATCGATACATCCAACCTCCATTGGGGTGCTTGGTTGAGTCGGTGTATGTCA

Reverse complement sequence

TGACATACACCGACTCAACCAAGCACCCCAATGGAGGTTGGATGTATCGATGCCTTGGCGAACACTTGCTGTATGGCTGCAATCAAATCTGTGGAGCTCT[G/A]
GGTAGGCTTTAATATGTAGCAAAGGAATAACAAATGCTCAAATCAGAGAATGCAAAGTTGAATAATTGTTCAAAGTCAAGCACCGTGCTGGTCCTAGGCT

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	64.80%	31.80%	1.71%	1.74%	NA
All Indica	2759	45.60%	52.70%	1.67%	0.00%	NA
All Japonica	1512	97.60%	1.00%	0.99%	0.40%	NA
Aus	269	94.40%	0.70%	1.12%	3.72%	NA
Indica I	595	60.20%	38.20%	1.68%	0.00%	NA
Indica II	465	21.70%	77.00%	1.29%	0.00%	NA
Indica III	913	43.00%	55.10%	1.86%	0.00%	NA
Indica Intermediate	786	51.80%	46.60%	1.65%	0.00%	NA
Temperate Japonica	767	99.10%	0.80%	0.00%	0.13%	NA
Tropical Japonica	504	95.80%	1.20%	2.58%	0.40%	NA
Japonica Intermediate	241	96.70%	1.20%	0.83%	1.24%	NA
VI/Aromatic	96	20.80%	2.10%	12.50%	64.58%	NA
Intermediate	90	58.90%	31.10%	5.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713647333	C -> DEL	N	N	silent_mutation	Average:12.105; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0713647333	C -> T	LOC_Os07g24070.1	upstream_gene_variant ; 237.0bp to feature; MODIFIER	silent_mutation	Average:12.105; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0713647333	C -> T	LOC_Os07g24050.1	downstream_gene_variant ; 4664.0bp to feature; MODIFIER	silent_mutation	Average:12.105; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0713647333	C -> T	LOC_Os07g24060.1	downstream_gene_variant ; 1219.0bp to feature; MODIFIER	silent_mutation	Average:12.105; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0713647333	C -> T	LOC_Os07g24080.1	downstream_gene_variant ; 3724.0bp to feature; MODIFIER	silent_mutation	Average:12.105; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0713647333	C -> T	LOC_Os07g24060-LOC_Os07g24070	intergenic_region ; MODIFIER	silent_mutation	Average:12.105; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713647333	NA	6.86E-08	mr1942	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
vg0713647333	NA	3.53E-07	mr1942	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