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Detailed information for vg1116842221:

Variant ID: vg1116842221 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16842221
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

GAAACATTAACCGTGCTAACCACAAACCAGAATGGGCAACAGCTGGACACTTTGTATAGCAAGGCTCATTGTGGTGTGCCAGACTGAGATGTGGCGGAGA[C/T]
AAGCCCATGGGGGTCGCTGGGGAGTCCATGCCTTGTTTTATAAGGGGGTGATTATGATCCAGGAACGGTGCACTGCTTTGAGTTGAGTTATGCGAGGGGT

Reverse complement sequence

ACCCCTCGCATAACTCAACTCAAAGCAGTGCACCGTTCCTGGATCATAATCACCCCCTTATAAAACAAGGCATGGACTCCCCAGCGACCCCCATGGGCTT[G/A]
TCTCCGCCACATCTCAGTCTGGCACACCACAATGAGCCTTGCTATACAAAGTGTCCAGCTGTTGCCCATTCTGGTTTGTGGTTAGCACGGTTAATGTTTC

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	68.40%	30.00%	1.40%	0.25%	NA
All Indica	2759	57.60%	41.20%	1.16%	0.00%	NA
All Japonica	1512	94.00%	3.90%	1.32%	0.79%	NA
Aus	269	22.70%	73.20%	4.09%	0.00%	NA
Indica I	595	81.20%	17.60%	1.18%	0.00%	NA
Indica II	465	52.90%	45.80%	1.29%	0.00%	NA
Indica III	913	43.90%	55.90%	0.22%	0.00%	NA
Indica Intermediate	786	58.50%	39.30%	2.16%	0.00%	NA
Temperate Japonica	767	97.90%	1.60%	0.26%	0.26%	NA
Tropical Japonica	504	90.10%	6.20%	2.38%	1.39%	NA
Japonica Intermediate	241	89.60%	6.60%	2.49%	1.24%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	75.60%	22.20%	2.22%	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
vg1116842221	C -> T	LOC_Os11g29074.1	upstream_gene_variant ; 948.0bp to feature; MODIFIER	silent_mutation	Average:32.239; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg1116842221	C -> T	LOC_Os11g29060.1	downstream_gene_variant ; 3433.0bp to feature; MODIFIER	silent_mutation	Average:32.239; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg1116842221	C -> T	LOC_Os11g29060-LOC_Os11g29074	intergenic_region ; MODIFIER	silent_mutation	Average:32.239; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg1116842221	C -> DEL	N	N	silent_mutation	Average:32.239; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116842221	2.57E-06	NA	mr1354_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
vg1116842221	3.14E-06	3.14E-06	mr1621_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