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Detailed information for vg0916498845:

Variant ID: vg0916498845 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 16498845
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

CCCTGCATTGGCTTCGATTTGCCATCGTGTCCATCATCCAACTGACACCGGTTTGCACCGGTATTCTCCTTGGTGCCCTCTCATTGAAATCAAGGGTAGC[A/G]
GCCATGTACTCAATGATGGCATCTTCTTCTTCGCTGCTTGTGTGACCGCCTCCATTCCAACTCGATCCACCCGCGCCGTAACTCATCGCCGATTTCCTTT

Reverse complement sequence

AAAGGAAATCGGCGATGAGTTACGGCGCGGGTGGATCGAGTTGGAATGGAGGCGGTCACACAAGCAGCGAAGAAGAAGATGCCATCATTGAGTACATGGC[T/C]
GCTACCCTTGATTTCAATGAGAGGGCACCAAGGAGAATACCGGTGCAAACCGGTGTCAGTTGGATGATGGACACGATGGCAAATCGAAGCCAATGCAGGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.10%	4.70%	2.54%	4.61%	NA
All Indica	2759	98.60%	0.30%	0.29%	0.76%	NA
All Japonica	1512	67.50%	13.60%	5.82%	13.03%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.50%	0.17%	0.00%	NA
Indica II	465	94.60%	0.40%	1.29%	3.66%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	0.40%	0.13%	0.51%	NA
Temperate Japonica	767	81.00%	3.10%	2.87%	13.04%	NA
Tropical Japonica	504	57.30%	19.20%	7.94%	15.48%	NA
Japonica Intermediate	241	46.10%	35.30%	10.79%	7.88%	NA
VI/Aromatic	96	74.00%	5.20%	20.83%	0.00%	NA
Intermediate	90	92.20%	3.30%	4.44%	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
vg0916498845	A -> G	LOC_Os09g27130.1	synonymous_variant ; p.Ala29Ala; LOW	synonymous_codon	Average:11.73; most accessible tissue: Minghui63 flower, score: 17.838	N	N	N	N
vg0916498845	A -> DEL	LOC_Os09g27130.1	N	frameshift_variant	Average:11.73; most accessible tissue: Minghui63 flower, score: 17.838	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0916498845	4.99E-08	2.62E-12	mr1064	Jap_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
vg0916498845	1.80E-06	1.95E-09	mr1534	Jap_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
vg0916498845	NA	7.77E-06	mr1745	Jap_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
vg0916498845	1.54E-06	3.52E-09	mr1064_2	Jap_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
vg0916498845	NA	2.84E-06	mr1745_2	Jap_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