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Detailed information for vg1206429009:

Variant ID: vg1206429009 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6429009
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.85, A: 0.16, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

AAACATTAGAATATATGTATATTGACAAACCTAAGAAAAGGAAAATAAAGTAAAAGGTACTAGCTCGTTGGAGATCATCGATGAAGATAGCAAGCTTGTG[T/A]
ATTGTACTTCCTCCGTTTTACAATATAAGTCATTCTAGCATTTTCCACATATATGTCTAGATTCATTAGCATCAATATGAATATGAGAAATGCTAGAATG

Reverse complement sequence

CATTCTAGCATTTCTCATATTCATATTGATGCTAATGAATCTAGACATATATGTGGAAAATGCTAGAATGACTTATATTGTAAAACGGAGGAAGTACAAT[A/T]
CACAAGCTTGCTATCTTCATCGATGATCTCCAACGAGCTAGTACCTTTTACTTTATTTTCCTTTTCTTAGGTTTGTCAATATACATATATTCTAATGTTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	25.30%	16.00%	0.13%	58.48%	NA
All Indica	2759	36.60%	7.50%	0.11%	55.74%	NA
All Japonica	1512	5.60%	30.60%	0.20%	63.62%	NA
Aus	269	3.30%	21.90%	0.00%	74.72%	NA
Indica I	595	86.20%	4.20%	0.00%	9.58%	NA
Indica II	465	20.90%	19.10%	0.22%	59.78%	NA
Indica III	913	11.40%	2.70%	0.11%	85.76%	NA
Indica Intermediate	786	37.80%	8.70%	0.13%	53.44%	NA
Temperate Japonica	767	8.70%	39.80%	0.26%	51.24%	NA
Tropical Japonica	504	2.20%	10.70%	0.20%	86.90%	NA
Japonica Intermediate	241	2.90%	42.70%	0.00%	54.36%	NA
VI/Aromatic	96	68.80%	10.40%	0.00%	20.83%	NA
Intermediate	90	30.00%	22.20%	0.00%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206429009	T -> DEL	N	N	silent_mutation	Average:71.522; most accessible tissue: Minghui63 panicle, score: 87.605	N	N	N	N
vg1206429009	T -> A	LOC_Os12g11830.1	upstream_gene_variant ; 2589.0bp to feature; MODIFIER	silent_mutation	Average:71.522; most accessible tissue: Minghui63 panicle, score: 87.605	N	N	N	N
vg1206429009	T -> A	LOC_Os12g11840.1	upstream_gene_variant ; 538.0bp to feature; MODIFIER	silent_mutation	Average:71.522; most accessible tissue: Minghui63 panicle, score: 87.605	N	N	N	N
vg1206429009	T -> A	LOC_Os12g11830-LOC_Os12g11840	intergenic_region ; MODIFIER	silent_mutation	Average:71.522; most accessible tissue: Minghui63 panicle, score: 87.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206429009	7.42E-08	NA	Heading_date	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652