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Detailed information for vg1115365932:

Variant ID: vg1115365932 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15365932
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTATACCTCTCAAGCTCGTGAAAGCTCGAGGCTTGGACGAGCCGAGTACAAGCTTACCTCTAAGCTCGGAGAATGATGAGGCTCAGTTCGAGCTCGGCT[C/A]
GAGTCTCTACTGAGCTCGAGCTTACACAGACAAGCACGCTCGAGCTCGGCTCGTTGACAACCCTATGTCTATCGCTTGACTGTCTATCACACCCGGAGTT

Reverse complement sequence

AACTCCGGGTGTGATAGACAGTCAAGCGATAGACATAGGGTTGTCAACGAGCCGAGCTCGAGCGTGCTTGTCTGTGTAAGCTCGAGCTCAGTAGAGACTC[G/T]
AGCCGAGCTCGAACTGAGCCTCATCATTCTCCGAGCTTAGAGGTAAGCTTGTACTCGGCTCGTCCAAGCCTCGAGCTTTCACGAGCTTGAGAGGTATAAT

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	97.40%	1.50%	1.02%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	92.10%	4.80%	3.17%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	85.40%	8.90%	5.74%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	1.20%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1115365932	C -> A	LOC_Os11g26795-LOC_Os11g26810	intergenic_region ; MODIFIER	silent_mutation	Average:55.044; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115365932	7.29E-07	NA	mr1091_2	Jap_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
vg1115365932	NA	3.18E-06	mr1138_2	Jap_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