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Detailed information for vg0618381087:

Variant ID: vg0618381087 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18381087
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.03, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

CCCCCGCGGAGAAGATGGAGCACTGGACCATGCATTTTGACGGATCAAAACGACTTTCGGGCACTGGAGCAGGAGTAGTTTTAATTTCCCCAACTGGAGA[G/A]
AGATTAAGCTATGTGCTTTGGATACATTTTTCGGCGTCCCACAATGTCGCCGAGTATGAGGCGCTCCTTCATGGACTGCGGATTGCAATTTCCCTAGGGA

Reverse complement sequence

TCCCTAGGGAAATTGCAATCCGCAGTCCATGAAGGAGCGCCTCATACTCGGCGACATTGTGGGACGCCGAAAAATGTATCCAAAGCACATAGCTTAATCT[C/T]
TCTCCAGTTGGGGAAATTAAAACTACTCCTGCTCCAGTGCCCGAAAGTCGTTTTGATCCGTCAAAATGCATGGTCCAGTGCTCCATCTTCTCCGCGGGGG

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	76.50%	0.30%	5.21%	17.94%	NA
All Indica	2759	67.60%	0.10%	6.78%	25.55%	NA
All Japonica	1512	90.90%	0.70%	2.65%	5.75%	NA
Aus	269	87.40%	0.70%	2.60%	9.29%	NA
Indica I	595	67.40%	0.00%	2.69%	29.92%	NA
Indica II	465	63.90%	0.20%	10.32%	25.59%	NA
Indica III	913	67.60%	0.10%	7.34%	24.97%	NA
Indica Intermediate	786	69.80%	0.10%	7.12%	22.90%	NA
Temperate Japonica	767	86.30%	0.50%	2.35%	10.82%	NA
Tropical Japonica	504	95.20%	1.00%	3.57%	0.20%	NA
Japonica Intermediate	241	96.30%	0.80%	1.66%	1.24%	NA
VI/Aromatic	96	69.80%	0.00%	9.38%	20.83%	NA
Intermediate	90	84.40%	0.00%	3.33%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618381087	G -> A	LOC_Os06g31630.1	downstream_gene_variant ; 1967.0bp to feature; MODIFIER	silent_mutation	Average:23.718; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N
vg0618381087	G -> A	LOC_Os06g31600-LOC_Os06g31630	intergenic_region ; MODIFIER	silent_mutation	Average:23.718; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N
vg0618381087	G -> DEL	N	N	silent_mutation	Average:23.718; most accessible tissue: Minghui63 young leaf, score: 47.146	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618381087	4.81E-06	NA	mr1124	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
vg0618381087	3.00E-08	3.00E-08	mr1861	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