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Detailed information for vg1117150680:

Variant ID: vg1117150680 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17150680
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TTGCACCCAGGAATTTGCTTTAATGAAGTCGGATCCCCCAATCGCTCAACGCCGATCTCCCCGCCACCAAACTGGGCAAGGGAGCGGAGGACCAAGAATT[C/A]
GGTCTGAAACTCAACCAGGTGCTTCTGATCCAGTTGGCCAGTCAGACTCTCGAAAGAGGAAACTGGTTCTGAGTGACGACGAAGCCGATGATACTACCAG

Reverse complement sequence

CTGGTAGTATCATCGGCTTCGTCGTCACTCAGAACCAGTTTCCTCTTTCGAGAGTCTGACTGGCCAACTGGATCAGAAGCACCTGGTTGAGTTTCAGACC[G/T]
AATTCTTGGTCCTCCGCTCCCTTGCCCAGTTTGGTGGCGGGGAGATCGGCGTTGAGCGATTGGGGGATCCGACTTCATTAAAGCAAATTCCTGGGTGCAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.50%	14.40%	0.66%	31.42%	NA
All Indica	2759	53.50%	23.90%	0.47%	22.11%	NA
All Japonica	1512	60.20%	0.20%	0.60%	39.02%	NA
Aus	269	29.40%	3.30%	1.86%	65.43%	NA
Indica I	595	33.80%	59.80%	0.50%	5.88%	NA
Indica II	465	52.70%	8.60%	0.65%	38.06%	NA
Indica III	913	67.30%	9.30%	0.11%	23.33%	NA
Indica Intermediate	786	53.10%	22.60%	0.76%	23.54%	NA
Temperate Japonica	767	87.20%	0.00%	0.39%	12.39%	NA
Tropical Japonica	504	33.50%	0.20%	0.79%	65.48%	NA
Japonica Intermediate	241	29.90%	0.80%	0.83%	68.46%	NA
VI/Aromatic	96	7.30%	2.10%	3.12%	87.50%	NA
Intermediate	90	61.10%	10.00%	1.11%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117150680	C -> A	LOC_Os11g29550.1	downstream_gene_variant ; 3757.0bp to feature; MODIFIER	silent_mutation	Average:22.251; most accessible tissue: Callus, score: 37.083	N	N	N	N
vg1117150680	C -> A	LOC_Os11g29570.1	downstream_gene_variant ; 2196.0bp to feature; MODIFIER	silent_mutation	Average:22.251; most accessible tissue: Callus, score: 37.083	N	N	N	N
vg1117150680	C -> A	LOC_Os11g29560.1	intron_variant ; MODIFIER	silent_mutation	Average:22.251; most accessible tissue: Callus, score: 37.083	N	N	N	N
vg1117150680	C -> DEL	N	N	silent_mutation	Average:22.251; most accessible tissue: Callus, score: 37.083	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117150680	NA	9.37E-07	mr1170	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
vg1117150680	NA	9.49E-06	mr1378	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
vg1117150680	NA	1.20E-08	mr1935	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