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Detailed information for vg0815545983:

Variant ID: vg0815545983 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 15545983
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGGCCCACTTGTCGGCGTCCCGAGAGAGGAGGGAGGGGCGGCTTGGGCCGGCCCACAAGGAGGAGGGGCCGCGGGAGAGGGATGGGCCGACGGCCCAAC[G/A]
AAGAAAAAGGAGGGAAAAGAAAAGAAAAAGAGAAAAAGGATTTTCCTGGGATTTAAAATTGCACTTTGGTGATTTTTAATTGGTTAAAATTATTTCCAAG

Reverse complement sequence

CTTGGAAATAATTTTAACCAATTAAAAATCACCAAAGTGCAATTTTAAATCCCAGGAAAATCCTTTTTCTCTTTTTCTTTTCTTTTCCCTCCTTTTTCTT[C/T]
GTTGGGCCGTCGGCCCATCCCTCTCCCGCGGCCCCTCCTCCTTGTGGGCCGGCCCAAGCCGCCCCTCCCTCCTCTCTCGGGACGCCGACAAGTGGGCCCC

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	12.00%	10.30%	7.47%	70.25%	NA
All Indica	2759	3.50%	0.20%	6.92%	89.38%	NA
All Japonica	1512	29.40%	31.10%	3.97%	35.52%	NA
Aus	269	3.70%	0.40%	34.20%	61.71%	NA
Indica I	595	5.70%	0.00%	0.84%	93.45%	NA
Indica II	465	4.50%	0.00%	5.38%	90.11%	NA
Indica III	913	0.90%	0.30%	12.92%	85.87%	NA
Indica Intermediate	786	4.20%	0.40%	5.47%	89.95%	NA
Temperate Japonica	767	33.10%	46.80%	6.13%	13.95%	NA
Tropical Japonica	504	17.90%	9.30%	1.59%	71.23%	NA
Japonica Intermediate	241	41.90%	26.60%	2.07%	29.46%	NA
VI/Aromatic	96	1.00%	1.00%	2.08%	95.83%	NA
Intermediate	90	16.70%	8.90%	8.89%	65.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0815545983	G -> A	LOC_Os08g25560.1	upstream_gene_variant ; 3787.0bp to feature; MODIFIER	silent_mutation	Average:60.734; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0815545983	G -> A	LOC_Os08g25560-LOC_Os08g25570	intergenic_region ; MODIFIER	silent_mutation	Average:60.734; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0815545983	G -> DEL	N	N	silent_mutation	Average:60.734; 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
vg0815545983	5.57E-07	5.57E-07	mr1806	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