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Detailed information for vg1117453139:

Variant ID: vg1117453139 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17453139
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

TATTGTCCTGGCATAACAAGAGAGTCTCTAAGCAAGCGAAATCACCGTCCTTCACTCCAGACCATTCTGACAATTCATACATCCAGGAAAAACTCAAGTT[G/C]
ACCAATGAGCGGAAAACTTTAACACTTTGATTTAGGCAGCAAAACTCTCGTCCAATGAATCGAAGATTATACATTCTGGAAATCTCCAAAGACTCAAGGG

Reverse complement sequence

CCCTTGAGTCTTTGGAGATTTCCAGAATGTATAATCTTCGATTCATTGGACGAGAGTTTTGCTGCCTAAATCAAAGTGTTAAAGTTTTCCGCTCATTGGT[C/G]
AACTTGAGTTTTTCCTGGATGTATGAATTGTCAGAATGGTCTGGAGTGAAGGACGGTGATTTCGCTTGCTTAGAGACTCTCTTGTTATGCCAGGACAATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.10%	27.10%	0.25%	2.56%	NA
All Indica	2759	96.80%	2.80%	0.00%	0.40%	NA
All Japonica	1512	17.50%	74.60%	0.79%	7.14%	NA
Aus	269	96.70%	3.30%	0.00%	0.00%	NA
Indica I	595	91.30%	8.70%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	98.60%	0.30%	0.00%	1.10%	NA
Indica Intermediate	786	97.50%	2.40%	0.00%	0.13%	NA
Temperate Japonica	767	3.10%	81.40%	1.56%	13.95%	NA
Tropical Japonica	504	40.70%	59.10%	0.00%	0.20%	NA
Japonica Intermediate	241	14.50%	85.50%	0.00%	0.00%	NA
VI/Aromatic	96	52.10%	47.90%	0.00%	0.00%	NA
Intermediate	90	75.60%	22.20%	0.00%	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
vg1117453139	G -> DEL	N	N	silent_mutation	Average:74.038; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N
vg1117453139	G -> C	LOC_Os11g30000.1	downstream_gene_variant ; 3804.0bp to feature; MODIFIER	silent_mutation	Average:74.038; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N
vg1117453139	G -> C	LOC_Os11g30020.1	downstream_gene_variant ; 3376.0bp to feature; MODIFIER	silent_mutation	Average:74.038; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N
vg1117453139	G -> C	LOC_Os11g30000-LOC_Os11g30020	intergenic_region ; MODIFIER	silent_mutation	Average:74.038; most accessible tissue: Minghui63 root, score: 86.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117453139	7.99E-06	NA	mr1182	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
vg1117453139	2.67E-06	NA	mr1182	Jap_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