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Detailed information for vg0617656510:

Variant ID: vg0617656510 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17656510
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: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGGTTACCCTCATCGTTGCCCTCCTCGTTCAGGTATTGGTTGGGATCCTCGTTTCCCTCCTCATCCACCTAGTACTGACTGCTGCCCTCTGCGATCGT[G/A]
TCTAACAGGATTTGTTCGTCATCGCAGTCTGCCATCTGTACGTGCAAAGAAAAAAAGACAGTGAGGTCATGCACATCGACATGTACAGGTCATACGTCTA

Reverse complement sequence

TAGACGTATGACCTGTACATGTCGATGTGCATGACCTCACTGTCTTTTTTTCTTTGCACGTACAGATGGCAGACTGCGATGACGAACAAATCCTGTTAGA[C/T]
ACGATCGCAGAGGGCAGCAGTCAGTACTAGGTGGATGAGGAGGGAAACGAGGATCCCAACCAATACCTGAACGAGGAGGGCAACGATGAGGGTAACCAGG

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	47.40%	5.10%	14.79%	32.71%	NA
All Indica	2759	21.90%	4.60%	20.41%	53.03%	NA
All Japonica	1512	97.30%	0.10%	0.79%	1.85%	NA
Aus	269	19.00%	40.90%	28.25%	11.90%	NA
Indica I	595	21.80%	0.20%	21.85%	56.13%	NA
Indica II	465	15.30%	17.80%	12.04%	54.84%	NA
Indica III	913	20.40%	0.80%	24.53%	54.33%	NA
Indica Intermediate	786	27.70%	4.70%	19.47%	48.09%	NA
Temperate Japonica	767	96.10%	0.00%	0.91%	3.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.20%	0.60%	NA
Japonica Intermediate	241	97.10%	0.40%	1.66%	0.83%	NA
VI/Aromatic	96	63.50%	0.00%	35.42%	1.04%	NA
Intermediate	90	56.70%	3.30%	15.56%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0617656510	G -> A	LOC_Os06g30520.1	synonymous_variant ; p.Asp524Asp; LOW	synonymous_codon	Average:52.562; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0617656510	G -> DEL	LOC_Os06g30520.1	N	frameshift_variant	Average:52.562; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617656510	NA	8.37E-07	mr1369	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
vg0617656510	6.86E-06	5.48E-08	mr1392	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
vg0617656510	NA	7.76E-06	mr1740_2	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
vg0617656510	7.00E-06	4.13E-09	mr1931_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
vg0617656510	NA	2.92E-06	mr1931_2	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