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Detailed information for vg0500736167:

Variant ID: vg0500736167 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 736167
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTGCTAGTTTATTTTTAGTTTCGCCGTACTATTAAGAGGGGTAATGACCTAGCAAAGAGATGATTTTAATTGCCACATTAGGTCATTGTGCATTTA[G/A]
ACTTGTGCTCGTTTTTCATCACACACACAATCACTTGGGATTTCACTGGTTTCGGCGTGACCAGGGGCAGTCAGACTGGCCACATAGTGGCGGTCTGACC

Reverse complement sequence

GGTCAGACCGCCACTATGTGGCCAGTCTGACTGCCCCTGGTCACGCCGAAACCAGTGAAATCCCAAGTGATTGTGTGTGTGATGAAAAACGAGCACAAGT[C/T]
TAAATGCACAATGACCTAATGTGGCAATTAAAATCATCTCTTTGCTAGGTCATTACCCCTCTTAATAGTACGGCGAAACTAAAAATAAACTAGCAAATTT

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	44.50%	33.10%	13.08%	9.31%	NA
All Indica	2759	66.30%	3.60%	21.28%	8.81%	NA
All Japonica	1512	4.20%	87.60%	0.20%	8.00%	NA
Aus	269	58.70%	30.10%	6.32%	4.83%	NA
Indica I	595	97.30%	0.70%	0.84%	1.18%	NA
Indica II	465	69.90%	7.70%	11.61%	10.75%	NA
Indica III	913	39.00%	3.30%	44.80%	12.92%	NA
Indica Intermediate	786	72.40%	3.80%	15.14%	8.65%	NA
Temperate Japonica	767	6.80%	92.70%	0.00%	0.52%	NA
Tropical Japonica	504	0.00%	79.00%	0.60%	20.44%	NA
Japonica Intermediate	241	5.00%	89.20%	0.00%	5.81%	NA
VI/Aromatic	96	25.00%	10.40%	8.33%	56.25%	NA
Intermediate	90	31.10%	55.60%	3.33%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0500736167	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500736167	G -> A	LOC_Os05g02300.1	upstream_gene_variant ; 2037.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500736167	G -> A	LOC_Os05g02280.1	downstream_gene_variant ; 3987.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500736167	G -> A	LOC_Os05g02290.1	downstream_gene_variant ; 889.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500736167	G -> A	LOC_Os05g02310.1	downstream_gene_variant ; 3479.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500736167	G -> A	LOC_Os05g02290-LOC_Os05g02300	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0500736167	NA	9.31E-06	mr1750	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
vg0500736167	NA	4.34E-06	mr1991	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
vg0500736167	NA	8.32E-07	mr1321_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
vg0500736167	1.15E-07	NA	mr1750_2	Ind_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