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Detailed information for vg0217163155:

Variant ID: vg0217163155 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17163155
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACTAGGTACACCTCACATGTCAACGATATAGAAAAGGAGTGGCGAAGTTAATTACCTATTGCTAGCCAGAGGGTGGTTCCAATTTTTATTATCCAAATC[T/C]
TTGTCAAGTTAGTGAAAAAAAATATGACATGCTTACTTAACCAAACATCGATCCCCTATATATATACCACGCAATGCGCCAGATAGTAGCCACATTCTCC

Reverse complement sequence

GGAGAATGTGGCTACTATCTGGCGCATTGCGTGGTATATATATAGGGGATCGATGTTTGGTTAAGTAAGCATGTCATATTTTTTTTCACTAACTTGACAA[A/G]
GATTTGGATAATAAAAATTGGAACCACCCTCTGGCTAGCAATAGGTAATTAACTTCGCCACTCCTTTTCTATATCGTTGACATGTGAGGTGTACCTAGTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.10%	2.10%	0.76%	0.00%	NA
All Indica	2759	95.10%	3.60%	1.27%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.10%	0.80%	2.02%	0.00%	NA
Indica II	465	96.10%	2.60%	1.29%	0.00%	NA
Indica III	913	93.60%	6.00%	0.33%	0.00%	NA
Indica Intermediate	786	94.70%	3.60%	1.78%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0217163155	T -> C	LOC_Os02g28980.1	upstream_gene_variant ; 2260.0bp to feature; MODIFIER	silent_mutation	Average:48.265; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0217163155	T -> C	LOC_Os02g29010.1	upstream_gene_variant ; 4262.0bp to feature; MODIFIER	silent_mutation	Average:48.265; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0217163155	T -> C	LOC_Os02g28990.1	downstream_gene_variant ; 652.0bp to feature; MODIFIER	silent_mutation	Average:48.265; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0217163155	T -> C	LOC_Os02g29000.1	downstream_gene_variant ; 2033.0bp to feature; MODIFIER	silent_mutation	Average:48.265; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N
vg0217163155	T -> C	LOC_Os02g28980-LOC_Os02g28990	intergenic_region ; MODIFIER	silent_mutation	Average:48.265; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217163155	1.30E-06	1.30E-06	mr1355	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