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Detailed information for vg0815631643:

Variant ID: vg0815631643 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 15631643
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAACATGTACTTTCTCTGTCCCAAAAAAAACTTAACCTAGAAGGGAATATGACCCCTTCTAAGACAACGAATCTGGACTACCTTTTGTCTGGGTTTATT[A/G]
TTCGAGGAGGGGTCACATTCCGTTCTAGATTGAATTTTTTGGAACAAAGGTACTACATGTTCTCCTACCGTCGGTCCTACCAGGATGCGACTCTTTCCAT

Reverse complement sequence

ATGGAAAGAGTCGCATCCTGGTAGGACCGACGGTAGGAGAACATGTAGTACCTTTGTTCCAAAAAATTCAATCTAGAACGGAATGTGACCCCTCCTCGAA[T/C]
AATAAACCCAGACAAAAGGTAGTCCAGATTCGTTGTCTTAGAAGGGGTCATATTCCCTTCTAGGTTAAGTTTTTTTTGGGACAGAGAAAGTACATGTTCT

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	74.80%	24.80%	0.06%	0.28%	NA
All Indica	2759	91.40%	8.10%	0.11%	0.40%	NA
All Japonica	1512	38.60%	61.40%	0.00%	0.00%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	95.50%	4.30%	0.22%	0.00%	NA
Indica III	913	84.20%	15.00%	0.11%	0.66%	NA
Indica Intermediate	786	91.10%	8.30%	0.13%	0.51%	NA
Temperate Japonica	767	18.80%	81.20%	0.00%	0.00%	NA
Tropical Japonica	504	72.60%	27.40%	0.00%	0.00%	NA
Japonica Intermediate	241	30.70%	69.30%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	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
vg0815631643	A -> G	LOC_Os08g25690.1	upstream_gene_variant ; 691.0bp to feature; MODIFIER	silent_mutation	Average:59.016; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0815631643	A -> G	LOC_Os08g25690-LOC_Os08g25700	intergenic_region ; MODIFIER	silent_mutation	Average:59.016; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0815631643	A -> DEL	N	N	silent_mutation	Average:59.016; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0815631643	2.23E-08	2.22E-11	mr1238	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
vg0815631643	NA	7.82E-07	mr1309	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
vg0815631643	NA	1.74E-10	mr1471	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
vg0815631643	NA	7.69E-06	mr1484	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
vg0815631643	3.01E-06	8.17E-09	mr1841	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
vg0815631643	3.06E-10	1.74E-13	mr1238_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
vg0815631643	1.31E-09	3.43E-13	mr1484_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
vg0815631643	NA	9.05E-06	mr1609_2	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
vg0815631643	1.46E-10	5.87E-14	mr1841_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
vg0815631643	NA	5.63E-08	mr1900_2	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
vg0815631643	2.39E-08	2.39E-08	mr1945_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