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Detailed information for vg1121618472:

Variant ID: vg1121618472 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21618472
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, A: 0.19, others allele: 0.00, population size: 47. )

Flanking Sequence (100 bp) in Reference Genome:

AATACGCACGGCGAGAACTCTTACACGACCAGATCTTACATGGTCTTTTGTCTCTACAGGATCTGACAAGGCCTTATCGGCTTTGGGTGTCCCCAGCCGA[C/A]
GATCCCTTAGGTTCCTCGGAGGCCTTGTCAAGACAGCGTAAAGGGACATAAGGACAGGTTTCAACGCTAGGTGTCATCAGGGTAAGGGATCATCGGGTGA

Reverse complement sequence

TCACCCGATGATCCCTTACCCTGATGACACCTAGCGTTGAAACCTGTCCTTATGTCCCTTTACGCTGTCTTGACAAGGCCTCCGAGGAACCTAAGGGATC[G/T]
TCGGCTGGGGACACCCAAAGCCGATAAGGCCTTGTCAGATCCTGTAGAGACAAAAGACCATGTAAGATCTGGTCGTGTAAGAGTTCTCGCCGTGCGTATT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.30%	1.00%	55.46%	13.25%	NA
All Indica	2759	10.20%	1.40%	80.86%	7.58%	NA
All Japonica	1512	71.60%	0.10%	4.89%	23.48%	NA
Aus	269	12.60%	2.60%	69.52%	15.24%	NA
Indica I	595	19.00%	0.50%	52.94%	27.56%	NA
Indica II	465	8.40%	1.30%	88.60%	1.72%	NA
Indica III	913	2.50%	2.40%	94.63%	0.44%	NA
Indica Intermediate	786	13.50%	0.90%	81.42%	4.20%	NA
Temperate Japonica	767	81.90%	0.00%	3.26%	14.86%	NA
Tropical Japonica	504	56.90%	0.20%	7.54%	35.32%	NA
Japonica Intermediate	241	69.30%	0.00%	4.56%	26.14%	NA
VI/Aromatic	96	3.10%	2.10%	88.54%	6.25%	NA
Intermediate	90	34.40%	0.00%	48.89%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121618472	C -> A	LOC_Os11g36630.1	downstream_gene_variant ; 436.0bp to feature; MODIFIER	silent_mutation	Average:12.915; most accessible tissue: Minghui63 flower, score: 16.541	N	N	N	N
vg1121618472	C -> A	LOC_Os11g36640.1	downstream_gene_variant ; 540.0bp to feature; MODIFIER	silent_mutation	Average:12.915; most accessible tissue: Minghui63 flower, score: 16.541	N	N	N	N
vg1121618472	C -> A	LOC_Os11g36630-LOC_Os11g36640	intergenic_region ; MODIFIER	silent_mutation	Average:12.915; most accessible tissue: Minghui63 flower, score: 16.541	N	N	N	N
vg1121618472	C -> DEL	N	N	silent_mutation	Average:12.915; most accessible tissue: Minghui63 flower, score: 16.541	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121618472	NA	2.59E-06	mr1622	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
vg1121618472	NA	5.25E-10	mr1986	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
vg1121618472	7.74E-06	NA	mr1718_2	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