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Detailed information for vg1224593986:

Variant ID: vg1224593986 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24593986
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, T: 0.03, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGCTTCGCTAACGTTATTGACGATGTGGTCTAACATGACTTAGGTCTTGTCTAGTTCAAAAAAATTTTGCCCAAAAACGTCACATCGAATCTTTGGAC[T/A]
CATGCATAGAGCATTAAATATAAATAAAAAATAATTGCACAGTTTGCATGGAAATCGAGAGACGAATCTTTTGAGCCTAATTAGTCCATGATTAGCCATA

Reverse complement sequence

TATGGCTAATCATGGACTAATTAGGCTCAAAAGATTCGTCTCTCGATTTCCATGCAAACTGTGCAATTATTTTTTATTTATATTTAATGCTCTATGCATG[A/T]
GTCCAAAGATTCGATGTGACGTTTTTGGGCAAAATTTTTTTGAACTAGACAAGACCTAAGTCATGTTAGACCACATCGTCAATAACGTTAGCGAAGCGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.80%	23.20%	0.23%	0.78%	NA
All Indica	2759	99.70%	0.20%	0.04%	0.04%	NA
All Japonica	1512	32.10%	66.10%	0.60%	1.19%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.50%	0.00%	0.13%	NA
Temperate Japonica	767	12.00%	87.20%	0.78%	0.00%	NA
Tropical Japonica	504	65.90%	30.20%	0.60%	3.37%	NA
Japonica Intermediate	241	25.30%	74.30%	0.00%	0.41%	NA
VI/Aromatic	96	14.60%	66.70%	1.04%	17.71%	NA
Intermediate	90	72.20%	26.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1224593986	T -> DEL	N	N	silent_mutation	Average:39.827; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg1224593986	T -> A	LOC_Os12g39800.1	upstream_gene_variant ; 2887.0bp to feature; MODIFIER	silent_mutation	Average:39.827; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg1224593986	T -> A	LOC_Os12g39800-LOC_Os12g39810	intergenic_region ; MODIFIER	silent_mutation	Average:39.827; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224593986	NA	9.13E-06	mr1029	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
vg1224593986	NA	1.20E-06	mr1157	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
vg1224593986	4.58E-06	NA	mr1219	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
vg1224593986	NA	8.62E-08	mr1271	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
vg1224593986	NA	8.77E-07	mr1446	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
vg1224593986	NA	3.98E-10	mr1790	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
vg1224593986	NA	3.22E-06	mr1096_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
vg1224593986	NA	3.90E-06	mr1121_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
vg1224593986	NA	4.97E-17	mr1790_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