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Detailed information for vg1109920086:

Variant ID: vg1109920086 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9920086
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCATAAGGGTCCTCCTCTTGACCCAGATCTGAAAAAGGGTTTATAAGAGCAAGGGTGAGTATTTACAATACTTAGCAAGTTATCACGGGAATATGTTATG[C/T]
ATTGACATATAATAGGGTTCTTTGCAAAAAGCAGTATTAGACAATCTAAAAAAGTTATAGCAGGAATTTATAAAACATATAAACTTTAGATTTCTAACCA

Reverse complement sequence

TGGTTAGAAATCTAAAGTTTATATGTTTTATAAATTCCTGCTATAACTTTTTTAGATTGTCTAATACTGCTTTTTGCAAAGAACCCTATTATATGTCAAT[G/A]
CATAACATATTCCCGTGATAACTTGCTAAGTATTGTAAATACTCACCCTTGCTCTTATAAACCCTTTTTCAGATCTGGGTCAAGAGGAGGACCCTTATGA

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	42.70%	0.10%	4.99%	52.14%	NA
All Indica	2759	16.40%	0.20%	2.61%	80.79%	NA
All Japonica	1512	96.00%	0.00%	0.00%	3.97%	NA
Aus	269	18.60%	0.00%	57.62%	23.79%	NA
Indica I	595	25.40%	0.00%	0.84%	73.78%	NA
Indica II	465	12.90%	0.00%	1.08%	86.02%	NA
Indica III	913	5.40%	0.70%	3.50%	90.47%	NA
Indica Intermediate	786	24.40%	0.00%	3.82%	71.76%	NA
Temperate Japonica	767	97.30%	0.00%	0.00%	2.74%	NA
Tropical Japonica	504	94.40%	0.00%	0.00%	5.56%	NA
Japonica Intermediate	241	95.40%	0.00%	0.00%	4.56%	NA
VI/Aromatic	96	22.90%	0.00%	3.12%	73.96%	NA
Intermediate	90	48.90%	0.00%	6.67%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109920086	C -> T	LOC_Os11g17760.1	upstream_gene_variant ; 4352.0bp to feature; MODIFIER	silent_mutation	Average:6.606; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1109920086	C -> T	LOC_Os11g17740.1	downstream_gene_variant ; 2120.0bp to feature; MODIFIER	silent_mutation	Average:6.606; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1109920086	C -> T	LOC_Os11g17740-LOC_Os11g17760	intergenic_region ; MODIFIER	silent_mutation	Average:6.606; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1109920086	C -> DEL	N	N	silent_mutation	Average:6.606; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109920086	3.83E-07	2.95E-07	mr1582_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