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Detailed information for vg0216275518:

Variant ID: vg0216275518 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 16275518
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCTATAAATTCCATAAACCATTTCTCGTATTCCAGAAAATTCCGATAAATCATTTCCTTGTCAAGAAATTCCAATTAAACTTCTAAAATTCATATCTCT[C/T]
GATCCGTAACTCCGATTGACTCCGTTCAGCTTCCAGTATTTCCGTAAAATTGAGATATATCTAATGGCACTATTAATTAGTCTAAATAGGATCTTTATTT

Reverse complement sequence

AAATAAAGATCCTATTTAGACTAATTAATAGTGCCATTAGATATATCTCAATTTTACGGAAATACTGGAAGCTGAACGGAGTCAATCGGAGTTACGGATC[G/A]
AGAGATATGAATTTTAGAAGTTTAATTGGAATTTCTTGACAAGGAAATGATTTATCGGAATTTTCTGGAATACGAGAAATGGTTTATGGAATTTATAGAA

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	85.00%	5.10%	7.47%	2.45%	NA
All Indica	2759	77.90%	8.00%	10.55%	3.55%	NA
All Japonica	1512	98.00%	0.50%	1.26%	0.20%	NA
Aus	269	85.90%	4.10%	6.32%	3.72%	NA
Indica I	595	78.00%	6.10%	13.95%	2.02%	NA
Indica II	465	80.00%	7.50%	8.39%	4.09%	NA
Indica III	913	76.00%	10.00%	9.53%	4.49%	NA
Indica Intermediate	786	78.90%	7.40%	10.43%	3.31%	NA
Temperate Japonica	767	96.30%	1.00%	2.22%	0.39%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	79.20%	0.00%	20.83%	0.00%	NA
Intermediate	90	84.40%	3.30%	6.67%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0216275518	C -> T	LOC_Os02g27500.1	upstream_gene_variant ; 2969.0bp to feature; MODIFIER	silent_mutation	Average:43.911; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg0216275518	C -> T	LOC_Os02g27500-LOC_Os02g27510	intergenic_region ; MODIFIER	silent_mutation	Average:43.911; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg0216275518	C -> DEL	N	N	silent_mutation	Average:43.911; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0216275518	1.40E-06	2.46E-06	Yield	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652