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Detailed information for vg0506600358:

Variant ID: vg0506600358 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6600358
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

CACCAATGACGAGAACTAGGGGGAAAATTTCCCTGTTGGGGCTAGGATTCGCCCCTACGAGACCAGAGGCAGGTGCGAGCATCAGTTACGCGAGGGTGAC[G/A]
TGGCGATGTCGTGACATGTGATTTACCTCTTCAAAAGTAGCCCATTTCAACAATATAAGCCCAGCTGACCTAGTAGATGGAGTAAGTAGCCCATATATAA

Reverse complement sequence

TTATATATGGGCTACTTACTCCATCTACTAGGTCAGCTGGGCTTATATTGTTGAAATGGGCTACTTTTGAAGAGGTAAATCACATGTCACGACATCGCCA[C/T]
GTCACCCTCGCGTAACTGATGCTCGCACCTGCCTCTGGTCTCGTAGGGGCGAATCCTAGCCCCAACAGGGAAATTTTCCCCCTAGTTCTCGTCATTGGTG

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	89.30%	5.60%	1.29%	3.79%	NA
All Indica	2759	86.70%	7.10%	1.59%	4.57%	NA
All Japonica	1512	97.20%	2.10%	0.66%	0.00%	NA
Aus	269	77.00%	1.10%	2.23%	19.70%	NA
Indica I	595	93.60%	0.80%	2.86%	2.69%	NA
Indica II	465	94.20%	4.30%	0.22%	1.29%	NA
Indica III	913	87.40%	9.50%	0.33%	2.74%	NA
Indica Intermediate	786	76.20%	10.80%	2.93%	10.05%	NA
Temperate Japonica	767	98.70%	0.80%	0.52%	0.00%	NA
Tropical Japonica	504	97.40%	2.60%	0.00%	0.00%	NA
Japonica Intermediate	241	92.10%	5.40%	2.49%	0.00%	NA
VI/Aromatic	96	66.70%	33.30%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	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
vg0506600358	G -> DEL	N	N	silent_mutation	Average:68.818; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0506600358	G -> A	LOC_Os05g11640.1	upstream_gene_variant ; 3595.0bp to feature; MODIFIER	silent_mutation	Average:68.818; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0506600358	G -> A	LOC_Os05g11630-LOC_Os05g11640	intergenic_region ; MODIFIER	silent_mutation	Average:68.818; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506600358	NA	2.71E-07	mr1229	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
vg0506600358	5.23E-06	3.90E-06	mr1316	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
vg0506600358	2.66E-06	2.66E-06	mr1393	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
vg0506600358	7.65E-06	7.65E-06	mr1464	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
vg0506600358	1.56E-06	1.56E-06	mr1605	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
vg0506600358	4.45E-06	4.32E-06	mr1775	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