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Detailed information for vg0316823783:

Variant ID: vg0316823783 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16823783
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

CACTCTCATTGTCACATAGGAGTGGAATCTTGGTGAAGTTGTAGCCAAAATCTTTTAGGGTTTGTTTCATCCAAAGGAGTTGGGCACAACAAGAACCGGC[G/A]
GCAACATATTCGGCTTTGGCGGTGGATAAAGCAATGGAATTTTGCTTCTTGGAGGACCAAGAAACAAGGGACCGCCCAAGGAATTGGCACGTCCCGGTTG

Reverse complement sequence

CAACCGGGACGTGCCAATTCCTTGGGCGGTCCCTTGTTTCTTGGTCCTCCAAGAAGCAAAATTCCATTGCTTTATCCACCGCCAAAGCCGAATATGTTGC[C/T]
GCCGGTTCTTGTTGTGCCCAACTCCTTTGGATGAAACAAACCCTAAAAGATTTTGGCTACAACTTCACCAAGATTCCACTCCTATGTGACAATGAGAGTG

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	93.10%	4.30%	1.48%	1.16%	NA
All Indica	2759	98.30%	0.60%	0.11%	1.01%	NA
All Japonica	1512	96.40%	3.40%	0.00%	0.20%	NA
Aus	269	20.10%	46.50%	24.54%	8.92%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	97.20%	0.50%	0.22%	2.08%	NA
Indica Intermediate	786	97.20%	1.50%	0.13%	1.15%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	89.50%	9.90%	0.00%	0.60%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	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
vg0316823783	G -> A	LOC_Os03g29520.1	synonymous_variant ; p.Ala1373Ala; LOW	synonymous_codon	Average:48.739; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0316823783	G -> DEL	LOC_Os03g29520.1	N	frameshift_variant	Average:48.739; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316823783	NA	8.74E-06	mr1312	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
vg0316823783	NA	4.97E-06	mr1049_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
vg0316823783	NA	2.36E-09	mr1344_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
vg0316823783	NA	2.56E-07	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