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Detailed information for vg0825088869:

Variant ID: vg0825088869 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25088869
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGCTAATGATGGATTAATTATACTTAATAAATTTGTCTTGCGGTTTATTGACAGATACTGTAATTAGTTTTTTTATTAGTACCCGAACATCCTATACG[A/G]
CACCTTATATAATACCCGATGTGATACGCCAAAACTTTAAACCTGCATCTAAGGGGGTGTTTAGATGGGGCTAAAATTTTTTAGCCCATGTCACATCGGA

Reverse complement sequence

TCCGATGTGACATGGGCTAAAAAATTTTAGCCCCATCTAAACACCCCCTTAGATGCAGGTTTAAAGTTTTGGCGTATCACATCGGGTATTATATAAGGTG[T/C]
CGTATAGGATGTTCGGGTACTAATAAAAAAACTAATTACAGTATCTGTCAATAAACCGCAAGACAAATTTATTAAGTATAATTAATCCATCATTAGCAAA

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	94.80%	3.60%	1.67%	0.00%	NA
All Indica	2759	99.70%	0.00%	0.33%	0.00%	NA
All Japonica	1512	84.60%	10.90%	4.50%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	0.00%	1.01%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	71.40%	20.10%	8.47%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	4.60%	1.24%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0825088869	A -> G	LOC_Os08g39630.1	upstream_gene_variant ; 654.0bp to feature; MODIFIER	silent_mutation	Average:61.903; most accessible tissue: Minghui63 flower, score: 78.041	N	N	N	N
vg0825088869	A -> G	LOC_Os08g39620-LOC_Os08g39630	intergenic_region ; MODIFIER	silent_mutation	Average:61.903; most accessible tissue: Minghui63 flower, score: 78.041	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825088869	NA	4.92E-06	mr1382	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
vg0825088869	NA	9.83E-06	mr1648	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
vg0825088869	NA	1.82E-06	mr1697	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
vg0825088869	7.52E-06	NA	mr1064_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
vg0825088869	NA	8.43E-06	mr1064_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
vg0825088869	NA	1.06E-06	mr1456_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
vg0825088869	NA	6.55E-06	mr1786_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
vg0825088869	5.59E-06	5.59E-06	mr1895_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
vg0825088869	3.78E-06	3.78E-06	mr1914_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