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Detailed information for vg0220738856:

Variant ID: vg0220738856 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20738856
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTATTGTCTTCGCAATGAAGCTCCTTGAATTTTGTGGCTCCACATCCATCAAGAAAATACGTCTCAAACAACTTGTAGATTCTGTATGTATAAACTTT[T/A]
GCTGCATGATTCAAAATATCACTGTGCTTTATAATACAAGCAGGAGGCTTTTGGCTGCACCGCGTGTCTTCATCGATCTCTTTTTCACGCCAATCTTCAG

Reverse complement sequence

CTGAAGATTGGCGTGAAAAAGAGATCGATGAAGACACGCGGTGCAGCCAAAAGCCTCCTGCTTGTATTATAAAGCACAGTGATATTTTGAATCATGCAGC[A/T]
AAAGTTTATACATACAGAATCTACAAGTTGTTTGAGACGTATTTTCTTGATGGATGTGGAGCCACAAAATTCAAGGAGCTTCATTGCGAAGACAATAACA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.90%	9.10%	0.00%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	75.70%	24.30%	0.00%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.10%	1.90%	0.00%	0.00%	NA
Temperate Japonica	767	73.50%	26.50%	0.00%	0.00%	NA
Tropical Japonica	504	79.80%	20.20%	0.00%	0.00%	NA
Japonica Intermediate	241	74.30%	25.70%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	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
vg0220738856	T -> A	LOC_Os02g34590.1	synonymous_variant ; p.Ala521Ala; LOW	synonymous_codon	Average:46.348; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220738856	8.76E-07	NA	Grain_weight	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