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Detailed information for vg0115686548:

Variant ID: vg0115686548 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15686548
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCAAGTCATCTTCGTCATCACCCCGTATCCCCATCAACCTCAACTCGTGGTTGCAAGAGGATGGATCGTCCATCGTCGGCACTCCGGTTCCTCAACGG[C/T]
GGCTACCGCTCAGCGACCTGCAAGACACACAAAATGGGAGAAGAGAGCAGTTAGGGACCAGAGAGAAGTAGAAAACCAAGAGAGGGGAGAGGAGCAGAGA

Reverse complement sequence

TCTCTGCTCCTCTCCCCTCTCTTGGTTTTCTACTTCTCTCTGGTCCCTAACTGCTCTCTTCTCCCATTTTGTGTGTCTTGCAGGTCGCTGAGCGGTAGCC[G/A]
CCGTTGAGGAACCGGAGTGCCGACGATGGACGATCCATCCTCTTGCAACCACGAGTTGAGGTTGATGGGGATACGGGGTGATGACGAAGATGACTTGGAG

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	57.10%	0.20%	7.83%	34.85%	NA
All Indica	2759	34.80%	0.30%	12.83%	52.12%	NA
All Japonica	1512	97.50%	0.10%	0.26%	2.18%	NA
Aus	269	40.50%	0.00%	2.60%	56.88%	NA
Indica I	595	24.20%	0.50%	11.26%	64.03%	NA
Indica II	465	54.20%	0.00%	15.27%	30.54%	NA
Indica III	913	28.50%	0.30%	12.92%	58.27%	NA
Indica Intermediate	786	38.50%	0.30%	12.47%	48.73%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	94.60%	0.00%	0.79%	4.56%	NA
Japonica Intermediate	241	97.90%	0.40%	0.00%	1.66%	NA
VI/Aromatic	96	93.80%	0.00%	2.08%	4.17%	NA
Intermediate	90	75.60%	0.00%	3.33%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115686548	C -> T	LOC_Os01g28040.1	upstream_gene_variant ; 26.0bp to feature; MODIFIER	silent_mutation	Average:15.646; most accessible tissue: Callus, score: 32.235	N	N	N	N
vg0115686548	C -> T	LOC_Os01g28040-LOC_Os01g28050	intergenic_region ; MODIFIER	silent_mutation	Average:15.646; most accessible tissue: Callus, score: 32.235	N	N	N	N
vg0115686548	C -> DEL	N	N	silent_mutation	Average:15.646; most accessible tissue: Callus, score: 32.235	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115686548	4.43E-06	4.43E-06	mr1521	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