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Detailed information for vg0500333563:

Variant ID: vg0500333563 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 333563
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:

AGACGATCGAGCAGTGGGAAAAAAAGGCTCACAGCACACGCTTTCGAGGGTTTGATCTTCAGCAAAATTCACAGCTCACGCAGGCGACCTCATGTATGTG[G/A]
AACAACCACTACTAGCCAACCGAGCGAGGGAACTTATCCATCAATTTACATATAAGCTACAATGTAAATTAATTATATATATTATATTTATATTGTAGTT

Reverse complement sequence

AACTACAATATAAATATAATATATATAATTAATTTACATTGTAGCTTATATGTAAATTGATGGATAAGTTCCCTCGCTCGGTTGGCTAGTAGTGGTTGTT[C/T]
CACATACATGAGGTCGCCTGCGTGAGCTGTGAATTTTGCTGAAGATCAAACCCTCGAAAGCGTGTGCTGTGAGCCTTTTTTTCCCACTGCTCGATCGTCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.80%	4.50%	0.19%	1.52%	NA
All Indica	2759	93.60%	6.20%	0.07%	0.18%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	62.50%	10.80%	2.23%	24.54%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	79.60%	20.20%	0.00%	0.22%	NA
Indica III	913	96.80%	3.00%	0.00%	0.22%	NA
Indica Intermediate	786	93.30%	6.20%	0.25%	0.25%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	91.10%	6.70%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0500333563	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500333563	G -> A	LOC_Os05g01560-LOC_Os05g01570	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0500333563	NA	3.39E-08	Grain_thickness	Ind_All	Not	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
vg0500333563	1.60E-06	2.22E-08	Grain_weight	Ind_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