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Detailed information for vg0816292104:

Variant ID: vg0816292104 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16292104
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTGTGACCCGTCAGTGATGTCTTTAACCCAACAAAAAAAAATTGAAAGACATAGCGTGCAACCCGTCACTGGTGTGAAAAACCTAGCCAAAAAAAATG[A/G]
CGCACGCTGCCATGGTGGTGCTCGTTGTCACAGTTGCTTTGCTCACACAAGAAATTCAAACCGATAGATCTCATATAGCACACATTCATAGAAGTCATAT

Reverse complement sequence

ATATGACTTCTATGAATGTGTGCTATATGAGATCTATCGGTTTGAATTTCTTGTGTGAGCAAAGCAACTGTGACAACGAGCACCACCATGGCAGCGTGCG[T/C]
CATTTTTTTTGGCTAGGTTTTTCACACCAGTGACGGGTTGCACGCTATGTCTTTCAATTTTTTTTTGTTGGGTTAAAGACATCACTGACGGGTCACAAAC

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	27.50%	0.10%	0.42%	71.96%	NA
All Indica	2759	3.60%	0.20%	0.33%	95.83%	NA
All Japonica	1512	70.20%	0.10%	0.53%	29.23%	NA
Aus	269	1.90%	0.00%	1.12%	97.03%	NA
Indica I	595	2.50%	0.00%	0.34%	97.14%	NA
Indica II	465	4.10%	0.00%	0.22%	95.70%	NA
Indica III	913	3.20%	0.00%	0.11%	96.71%	NA
Indica Intermediate	786	4.70%	0.80%	0.64%	93.89%	NA
Temperate Japonica	767	97.80%	0.00%	0.00%	2.22%	NA
Tropical Japonica	504	27.60%	0.20%	1.59%	70.63%	NA
Japonica Intermediate	241	71.40%	0.00%	0.00%	28.63%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	47.80%	0.00%	0.00%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816292104	A -> G	LOC_Os08g26800-LOC_Os08g26810	intergenic_region ; MODIFIER	silent_mutation	Average:5.535; most accessible tissue: Callus, score: 14.201	N	N	N	N
vg0816292104	A -> DEL	N	N	silent_mutation	Average:5.535; most accessible tissue: Callus, score: 14.201	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816292104	NA	2.95E-06	mr1233	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
vg0816292104	NA	1.75E-06	mr1345	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
vg0816292104	2.15E-07	2.15E-07	mr1362	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
vg0816292104	1.43E-06	4.27E-08	mr1653	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
vg0816292104	2.85E-07	2.85E-07	mr1849	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
vg0816292104	NA	3.18E-07	mr1866	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