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Detailed information for vg0618487499:

Variant ID: vg0618487499 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18487499
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.41, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

ACCAGCAATGATGGTCGAGTTGTAACTGTTCATGCATTGTCTTCTGAGTCTTTAAGGTCAAGTCTGAACCAAATGACTTTGGAAGAGATTCCTATAGTCC[A/G]
GGTGTGGACCCCCGTTTTTATAATAGGAATCATTCGTGTAAACAGTACCATTTCCCTGGATCAAGTAGTCTTGTACACACGAGTTCATAGCTGAAATACC

Reverse complement sequence

GGTATTTCAGCTATGAACTCGTGTGTACAAGACTACTTGATCCAGGGAAATGGTACTGTTTACACGAATGATTCCTATTATAAAAACGGGGGTCCACACC[T/C]
GGACTATAGGAATCTCTTCCAAAGTCATTTGGTTCAGACTTGACCTTAAAGACTCAGAAGACAATGCATGAACAGTTACAACTCGACCATCATTGCTGGT

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	36.40%	5.80%	0.53%	57.22%	NA
All Indica	2759	13.10%	3.00%	0.83%	83.07%	NA
All Japonica	1512	86.20%	6.10%	0.07%	7.67%	NA
Aus	269	5.90%	0.00%	0.37%	93.68%	NA
Indica I	595	24.70%	3.50%	0.67%	71.09%	NA
Indica II	465	14.60%	1.10%	0.43%	83.87%	NA
Indica III	913	2.80%	1.50%	0.77%	94.85%	NA
Indica Intermediate	786	15.40%	5.30%	1.27%	77.99%	NA
Temperate Japonica	767	87.50%	6.90%	0.13%	5.48%	NA
Tropical Japonica	504	84.70%	3.40%	0.00%	11.90%	NA
Japonica Intermediate	241	85.10%	9.10%	0.00%	5.81%	NA
VI/Aromatic	96	2.10%	90.60%	0.00%	7.29%	NA
Intermediate	90	43.30%	15.60%	0.00%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618487499	A -> G	LOC_Os06g31830.1	missense_variant ; p.Gln691Arg; MODERATE	nonsynonymous_codon ; Q691W	Average:5.905; most accessible tissue: Callus, score: 15.962	unknown	unknown	DELETERIOUS	0.01
vg0618487499	A -> G	LOC_Os06g31830.1	missense_variant ; p.Gln691Arg; MODERATE	nonsynonymous_codon ; Q691R	Average:5.905; most accessible tissue: Callus, score: 15.962	unknown	unknown	TOLERATED	1.00
vg0618487499	A -> DEL	LOC_Os06g31830.1	N	frameshift_variant	Average:5.905; most accessible tissue: Callus, score: 15.962	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618487499	NA	9.99E-08	mr1169_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
vg0618487499	6.82E-06	NA	mr1281_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
vg0618487499	1.64E-06	1.64E-06	mr1281_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
vg0618487499	NA	2.30E-09	mr1829_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
vg0618487499	2.39E-06	NA	mr1842_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
vg0618487499	5.34E-06	7.88E-07	mr1842_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