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Detailed information for vg0816195208:

Variant ID: vg0816195208 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16195208
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGACATGTAATGGGGGGATCCCCAAAAAATTTTATGAATCAATACAATTGCTTTTACATTCCAACTACTGTTGAGAGAACCATGCCTTTCGACGTGGCA[T/G]
AGTTGTCCATTCGACAACAGCTGGCACCGTCCGTGGGGAACCCAGACCGAAAGGGCGAAATGGGACCCCTTTTGCCACACCCACACCCTTCGCCACAGTA

Reverse complement sequence

TACTGTGGCGAAGGGTGTGGGTGTGGCAAAAGGGGTCCCATTTCGCCCTTTCGGTCTGGGTTCCCCACGGACGGTGCCAGCTGTTGTCGAATGGACAACT[A/C]
TGCCACGTCGAAAGGCATGGTTCTCTCAACAGTAGTTGGAATGTAAAAGCAATTGTATTGATTCATAAAATTTTTTGGGGATCCCCCCATTACATGTCCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.50%	2.50%	6.18%	49.79%	NA
All Indica	2759	24.30%	0.00%	8.05%	67.63%	NA
All Japonica	1512	67.90%	7.60%	2.78%	21.69%	NA
Aus	269	42.00%	0.40%	8.55%	49.07%	NA
Indica I	595	19.30%	0.00%	11.93%	68.74%	NA
Indica II	465	26.00%	0.00%	6.24%	67.74%	NA
Indica III	913	24.20%	0.00%	6.46%	69.33%	NA
Indica Intermediate	786	27.20%	0.00%	8.02%	64.76%	NA
Temperate Japonica	767	81.50%	12.90%	3.91%	1.69%	NA
Tropical Japonica	504	46.60%	0.00%	1.19%	52.18%	NA
Japonica Intermediate	241	69.30%	6.60%	2.49%	21.58%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	66.70%	2.20%	4.44%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816195208	T -> G	LOC_Os08g26620.1	upstream_gene_variant ; 1647.0bp to feature; MODIFIER	silent_mutation	Average:15.236; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0816195208	T -> G	LOC_Os08g26630.1	downstream_gene_variant ; 212.0bp to feature; MODIFIER	silent_mutation	Average:15.236; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0816195208	T -> G	LOC_Os08g26630-LOC_Os08g26650	intergenic_region ; MODIFIER	silent_mutation	Average:15.236; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0816195208	T -> DEL	N	N	silent_mutation	Average:15.236; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816195208	4.35E-06	3.92E-07	mr1126	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