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Detailed information for vg0613088863:

Variant ID: vg0613088863 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13088863
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ACCGATTGGGAAGAGGAACTCTCTCAAACCACTCAGGGTAAGGCTGCCGATACAAGCTTCCAGTCTCTTTTGGTTTAAGCCCAAACTGTTCCCTCATTAC[G/A]
TCGGCAATCACATCGGCCCATGGTCGCTGCTGAGCTGCTGCTTGTGGCTGTTGCTGCATGGGCTCAAACTGACCATACTGAGATGCGAACTGAGGTTGAG

Reverse complement sequence

CTCAACCTCAGTTCGCATCTCAGTATGGTCAGTTTGAGCCCATGCAGCAACAGCCACAAGCAGCAGCTCAGCAGCGACCATGGGCCGATGTGATTGCCGA[C/T]
GTAATGAGGGAACAGTTTGGGCTTAAACCAAAAGAGACTGGAAGCTTGTATCGGCAGCCTTACCCTGAGTGGTTTGAGAGAGTTCCTCTTCCCAATCGGT

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	89.70%	9.70%	0.13%	0.42%	NA
All Indica	2759	88.00%	12.00%	0.04%	0.00%	NA
All Japonica	1512	99.40%	0.50%	0.07%	0.00%	NA
Aus	269	50.60%	40.90%	1.49%	7.06%	NA
Indica I	595	87.10%	12.90%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	83.10%	16.80%	0.11%	0.00%	NA
Indica Intermediate	786	87.90%	12.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	0.00%	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
vg0613088863	G -> A	LOC_Os06g22520.1	synonymous_variant ; p.Asp377Asp; LOW	synonymous_codon	Average:48.226; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N
vg0613088863	G -> DEL	LOC_Os06g22520.1	N	frameshift_variant	Average:48.226; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613088863	NA	3.39E-06	mr1043	Ind_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
vg0613088863	1.74E-06	NA	mr1298	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
vg0613088863	NA	5.69E-07	mr1738	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
vg0613088863	NA	3.52E-06	mr1835	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