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Detailed information for vg0811925390:

Variant ID: vg0811925390 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11925390
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGATTTAATTGCAACGAATTTAATGGTACAATCGGATCATGATTTGAATAAGTAATTTAAGAGAAAAATCACTTGAAAGTAGTTTTTGCACGTAAATCG[G/A]
GCGCCCGACGCTTAGGGCCTTCCAAATAGTTACTACCAGATTACAAACTTATTGCTGGTAGTAAGGGAATATGATGGGTCCCACCTCACTTTTTTAAGTC

Reverse complement sequence

GACTTAAAAAAGTGAGGTGGGACCCATCATATTCCCTTACTACCAGCAATAAGTTTGTAATCTGGTAGTAACTATTTGGAAGGCCCTAAGCGTCGGGCGC[C/T]
CGATTTACGTGCAAAAACTACTTTCAAGTGATTTTTCTCTTAAATTACTTATTCAAATCATGATCCGATTGTACCATTAAATTCGTTGCAATTAAATCTT

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	81.00%	0.50%	11.30%	7.15%	NA
All Indica	2759	73.10%	0.80%	18.01%	8.12%	NA
All Japonica	1512	98.10%	0.10%	0.93%	0.93%	NA
Aus	269	60.60%	0.00%	3.35%	36.06%	NA
Indica I	595	62.90%	1.00%	31.60%	4.54%	NA
Indica II	465	75.90%	0.40%	17.42%	6.24%	NA
Indica III	913	78.30%	0.70%	10.62%	10.41%	NA
Indica Intermediate	786	73.00%	1.00%	16.67%	9.29%	NA
Temperate Japonica	767	99.20%	0.00%	0.39%	0.39%	NA
Tropical Japonica	504	96.20%	0.20%	1.98%	1.59%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	93.80%	1.00%	5.21%	0.00%	NA
Intermediate	90	86.70%	0.00%	10.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0811925390	G -> A	LOC_Os08g19920.1	upstream_gene_variant ; 3771.0bp to feature; MODIFIER	silent_mutation	Average:59.816; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0811925390	G -> A	LOC_Os08g19910.1	downstream_gene_variant ; 1532.0bp to feature; MODIFIER	silent_mutation	Average:59.816; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0811925390	G -> A	LOC_Os08g19890-LOC_Os08g19910	intergenic_region ; MODIFIER	silent_mutation	Average:59.816; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0811925390	G -> DEL	N	N	silent_mutation	Average:59.816; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811925390	NA	9.26E-09	mr1509_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
vg0811925390	NA	5.67E-09	mr1558_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