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Detailed information for vg1110114810:

Variant ID: vg1110114810 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10114810
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

CATATAGTATCCATCTAGAAGTCATAATCATGAAATAATCACGGATATCCAAACAAACAACCCGAAACCAAAACCGACACAGCGTCGGCCGGTCAGACCG[C/T]
GAGCTGCGCCGGTCTGACCGCGCGATACACGCCAGTCTGACCGGCACACACTACCCGGTTTGACCGGTCCACATAAAATAATGAACCTGCGATTCACCTG

Reverse complement sequence

CAGGTGAATCGCAGGTTCATTATTTTATGTGGACCGGTCAAACCGGGTAGTGTGTGCCGGTCAGACTGGCGTGTATCGCGCGGTCAGACCGGCGCAGCTC[G/A]
CGGTCTGACCGGCCGACGCTGTGTCGGTTTTGGTTTCGGGTTGTTTGTTTGGATATCCGTGATTATTTCATGATTATGACTTCTAGATGGATACTATATG

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	72.50%	25.10%	0.83%	1.54%	NA
All Indica	2759	57.70%	41.10%	1.16%	0.04%	NA
All Japonica	1512	97.70%	1.50%	0.20%	0.66%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	73.80%	23.40%	2.86%	0.00%	NA
Indica II	465	13.10%	86.20%	0.65%	0.00%	NA
Indica III	913	70.10%	29.60%	0.33%	0.00%	NA
Indica Intermediate	786	57.60%	41.10%	1.15%	0.13%	NA
Temperate Japonica	767	97.40%	2.20%	0.26%	0.13%	NA
Tropical Japonica	504	99.00%	0.60%	0.20%	0.20%	NA
Japonica Intermediate	241	95.90%	0.80%	0.00%	3.32%	NA
VI/Aromatic	96	31.20%	3.10%	3.12%	62.50%	NA
Intermediate	90	65.60%	31.10%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110114810	C -> T	LOC_Os11g17990.1	upstream_gene_variant ; 1055.0bp to feature; MODIFIER	silent_mutation	Average:34.511; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1110114810	C -> T	LOC_Os11g18000.1	upstream_gene_variant ; 1684.0bp to feature; MODIFIER	silent_mutation	Average:34.511; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1110114810	C -> T	LOC_Os11g17990-LOC_Os11g18000	intergenic_region ; MODIFIER	silent_mutation	Average:34.511; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1110114810	C -> DEL	N	N	silent_mutation	Average:34.511; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110114810	NA	4.54E-06	mr1872	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
vg1110114810	1.80E-06	1.80E-06	mr1872	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