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Detailed information for vg0612813818:

Variant ID: vg0612813818 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12813818
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: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTTTCTCACGTGATGCAATGATCCGCCGGTCACACCCCTCACGAATATATAGGATCCATCACTCGGGCCTCCAAGACCCGTAGGACTCCTGTTCGGAT[C/T]
CCTATCCGAATTAAGCTCATATTGGATCTCCATCCAATCCCCTTATTCCGGCCCATTAAACGTGCGACCCTGTAGGTTCATGTACACTCGGCTGTAACCC

Reverse complement sequence

GGGTTACAGCCGAGTGTACATGAACCTACAGGGTCGCACGTTTAATGGGCCGGAATAAGGGGATTGGATGGAGATCCAATATGAGCTTAATTCGGATAGG[G/A]
ATCCGAACAGGAGTCCTACGGGTCTTGGAGGCCCGAGTGATGGATCCTATATATTCGTGAGGGGTGTGACCGGCGGATCATTGCATCACGTGAGAAACCC

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	92.90%	5.80%	0.04%	1.25%	NA
All Indica	2759	96.50%	3.20%	0.07%	0.22%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	31.20%	67.70%	0.00%	1.12%	NA
Indica I	595	97.10%	2.70%	0.17%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	97.20%	2.60%	0.00%	0.22%	NA
Indica Intermediate	786	94.40%	5.00%	0.13%	0.51%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	50.00%	1.00%	0.00%	48.96%	NA
Intermediate	90	93.30%	3.30%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0612813818	C -> T	LOC_Os06g22080.1	downstream_gene_variant ; 1323.0bp to feature; MODIFIER	silent_mutation	Average:65.017; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg0612813818	C -> T	LOC_Os06g22090.1	downstream_gene_variant ; 976.0bp to feature; MODIFIER	silent_mutation	Average:65.017; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg0612813818	C -> T	LOC_Os06g22080.3	downstream_gene_variant ; 1323.0bp to feature; MODIFIER	silent_mutation	Average:65.017; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg0612813818	C -> T	LOC_Os06g22080-LOC_Os06g22090	intergenic_region ; MODIFIER	silent_mutation	Average:65.017; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg0612813818	C -> DEL	N	N	silent_mutation	Average:65.017; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612813818	NA	1.65E-06	mr1207	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
vg0612813818	NA	6.77E-07	mr1556	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
vg0612813818	3.04E-06	NA	mr1509_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