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Detailed information for vg0118364509:

Variant ID: vg0118364509 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18364509
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: 123. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCGTTGTCTCTCTGTTTCCTCGGTTCTGTTCATCCCGCGCGAACGGATGATCGGAATGAGCAGGTGCCTCTGAAACTCCGTCCGCTTGAGAACCTGCA[C/T]
GGGTAGGCAGGCGATCAAGTTTTTGGGTAGCGCTTCAAGCGCGACTGCTCTGCATCATCTTCACCAACATGTCAACAACCGGCGACAACAACAACACTGG

Reverse complement sequence

CCAGTGTTGTTGTTGTCGCCGGTTGTTGACATGTTGGTGAAGATGATGCAGAGCAGTCGCGCTTGAAGCGCTACCCAAAAACTTGATCGCCTGCCTACCC[G/A]
TGCAGGTTCTCAAGCGGACGGAGTTTCAGAGGCACCTGCTCATTCCGATCATCCGTTCGCGCGGGATGAACAGAACCGAGGAAACAGAGAGACAACGCAG

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	76.30%	23.70%	0.02%	0.00%	NA
All Indica	2759	60.10%	39.80%	0.04%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	53.40%	46.40%	0.17%	0.00%	NA
Indica II	465	59.80%	40.20%	0.00%	0.00%	NA
Indica III	913	57.70%	42.30%	0.00%	0.00%	NA
Indica Intermediate	786	68.20%	31.80%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0118364509	C -> T	LOC_Os01g33324.1	downstream_gene_variant ; 1229.0bp to feature; MODIFIER	silent_mutation	Average:47.29; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg0118364509	C -> T	LOC_Os01g33350.1	downstream_gene_variant ; 447.0bp to feature; MODIFIER	silent_mutation	Average:47.29; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg0118364509	C -> T	LOC_Os01g33324-LOC_Os01g33350	intergenic_region ; MODIFIER	silent_mutation	Average:47.29; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118364509	NA	6.89E-07	mr1349	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
vg0118364509	1.01E-06	1.01E-06	mr1349	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