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Detailed information for vg0827077651:

Variant ID: vg0827077651 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27077651
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCCTCTATCTATCAAAACTGGTGCAAACAATGTCCCTCGGTGGTTTTGGCTGACGTGGCGCCTACATGGCGGTTTTGACCGAGTCTTTGTCCTATGTG[A/G]
TGCTTACGTGGCATTAGAAAAAACAAAAATAAAAAAATATGTGGGACCCCTATGTCATTCACACACACAAAAAAAGTATTGTGGGACCCACATGTCATCC

Reverse complement sequence

GGATGACATGTGGGTCCCACAATACTTTTTTTGTGTGTGTGAATGACATAGGGGTCCCACATATTTTTTTATTTTTGTTTTTTCTAATGCCACGTAAGCA[T/C]
CACATAGGACAAAGACTCGGTCAAAACCGCCATGTAGGCGCCACGTCAGCCAAAACCACCGAGGGACATTGTTTGCACCAGTTTTGATAGATAGAGGAGT

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	45.10%	33.40%	0.19%	21.31%	NA
All Indica	2759	64.90%	0.90%	0.25%	34.00%	NA
All Japonica	1512	4.30%	95.00%	0.07%	0.60%	NA
Aus	269	84.40%	0.40%	0.00%	15.24%	NA
Indica I	595	71.60%	0.80%	0.00%	27.56%	NA
Indica II	465	64.30%	0.40%	0.22%	35.05%	NA
Indica III	913	63.50%	0.40%	0.33%	35.71%	NA
Indica Intermediate	786	61.70%	1.70%	0.38%	36.26%	NA
Temperate Japonica	767	2.30%	96.90%	0.00%	0.78%	NA
Tropical Japonica	504	7.50%	92.10%	0.20%	0.20%	NA
Japonica Intermediate	241	3.70%	95.40%	0.00%	0.83%	NA
VI/Aromatic	96	11.50%	83.30%	0.00%	5.21%	NA
Intermediate	90	41.10%	42.20%	1.11%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0827077651	A -> G	LOC_Os08g42810.1	upstream_gene_variant ; 2323.0bp to feature; MODIFIER	silent_mutation	Average:66.841; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0827077651	A -> G	LOC_Os08g42830.1	downstream_gene_variant ; 3034.0bp to feature; MODIFIER	silent_mutation	Average:66.841; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0827077651	A -> G	LOC_Os08g42820.1	intron_variant ; MODIFIER	silent_mutation	Average:66.841; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0827077651	A -> DEL	N	N	silent_mutation	Average:66.841; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827077651	NA	5.76E-08	mr1222	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
vg0827077651	NA	9.48E-07	mr1245	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
vg0827077651	NA	1.92E-06	mr1424	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
vg0827077651	NA	1.52E-15	mr1830	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
vg0827077651	NA	7.69E-06	mr1857	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
vg0827077651	NA	1.33E-06	mr1881	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
vg0827077651	NA	1.02E-08	mr1986	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