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Detailed information for vg1108502161:

Variant ID: vg1108502161 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8502161
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGACAGAAAGGTGTTATGCTGTTTTTGTAAGCTTTTTTAGGCTACGAAAGCTGTCTGGGTTAACTTGGAATGACTTGTTTTTTACCATAGTCATTTCCT[T/C]
GGTATGTTATATGCCTGTTTTCATTATGGTAAATAGTCATAGCTTAGGCTAGTAGACTTATTCATTACCATATTTTTTATAATATTTGGTGGGTAATCTT

Reverse complement sequence

AAGATTACCCACCAAATATTATAAAAAATATGGTAATGAATAAGTCTACTAGCCTAAGCTATGACTATTTACCATAATGAAAACAGGCATATAACATACC[A/G]
AGGAAATGACTATGGTAAAAAACAAGTCATTCCAAGTTAACCCAGACAGCTTTCGTAGCCTAAAAAAGCTTACAAAAACAGCATAACACCTTTCTGTCGG

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	56.30%	0.50%	2.22%	41.01%	NA
All Indica	2759	31.40%	0.80%	3.55%	64.30%	NA
All Japonica	1512	91.70%	0.00%	0.46%	7.80%	NA
Aus	269	95.20%	0.00%	0.00%	4.83%	NA
Indica I	595	20.80%	0.50%	2.69%	75.97%	NA
Indica II	465	31.80%	1.10%	3.23%	63.87%	NA
Indica III	913	34.60%	0.70%	4.93%	59.80%	NA
Indica Intermediate	786	35.20%	1.00%	2.80%	60.94%	NA
Temperate Japonica	767	98.20%	0.00%	0.26%	1.56%	NA
Tropical Japonica	504	84.30%	0.00%	0.60%	15.08%	NA
Japonica Intermediate	241	86.70%	0.00%	0.83%	12.45%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	66.70%	0.00%	0.00%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108502161	T -> DEL	N	N	silent_mutation	Average:7.339; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1108502161	T -> C	LOC_Os11g15100.1	upstream_gene_variant ; 539.0bp to feature; MODIFIER	silent_mutation	Average:7.339; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1108502161	T -> C	LOC_Os11g15090.1	downstream_gene_variant ; 3763.0bp to feature; MODIFIER	silent_mutation	Average:7.339; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1108502161	T -> C	LOC_Os11g15110.1	downstream_gene_variant ; 3885.0bp to feature; MODIFIER	silent_mutation	Average:7.339; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1108502161	T -> C	LOC_Os11g15100-LOC_Os11g15110	intergenic_region ; MODIFIER	silent_mutation	Average:7.339; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108502161	NA	2.74E-06	mr1807	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
vg1108502161	NA	6.77E-06	mr1923_2	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