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Detailed information for vg0817358920:

Variant ID: vg0817358920 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17358920
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTAGAACCAATTGGTGTTGAAATTGGCCTGCAACTCTCCATCTTGAACCGTCTCAAAAGATCCTTTGTGTACTTCGTTTGATGCACAAATATACCTTGAG[A/G]
TGTTTGCTTAATTTGCAATCCCAAAAAATACGATAACTCACCCATCATGCTCATCTCAAATTCCCTGCGCATAGTCTCAGCAAACACCACAACCAAAGCG

Reverse complement sequence

CGCTTTGGTTGTGGTGTTTGCTGAGACTATGCGCAGGGAATTTGAGATGAGCATGATGGGTGAGTTATCGTATTTTTTGGGATTGCAAATTAAGCAAACA[T/C]
CTCAAGGTATATTTGTGCATCAAACGAAGTACACAAAGGATCTTTTGAGACGGTTCAAGATGGAGAGTTGCAGGCCAATTTCAACACCAATTGGTTCTAC

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	36.00%	6.30%	1.14%	56.60%	NA
All Indica	2759	4.90%	6.90%	1.85%	86.44%	NA
All Japonica	1512	94.00%	2.00%	0.07%	3.97%	NA
Aus	269	1.50%	27.50%	0.37%	70.63%	NA
Indica I	595	8.10%	3.00%	1.34%	87.56%	NA
Indica II	465	4.10%	5.80%	1.51%	88.60%	NA
Indica III	913	1.80%	13.10%	2.08%	83.02%	NA
Indica Intermediate	786	6.50%	3.10%	2.16%	88.30%	NA
Temperate Japonica	767	95.30%	3.80%	0.00%	0.91%	NA
Tropical Japonica	504	90.70%	0.20%	0.20%	8.93%	NA
Japonica Intermediate	241	96.70%	0.00%	0.00%	3.32%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	57.80%	4.40%	1.11%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817358920	A -> G	LOC_Os08g28450.1	downstream_gene_variant ; 852.0bp to feature; MODIFIER	silent_mutation	Average:7.291; most accessible tissue: Callus, score: 23.893	N	N	N	N
vg0817358920	A -> G	LOC_Os08g28430-LOC_Os08g28450	intergenic_region ; MODIFIER	silent_mutation	Average:7.291; most accessible tissue: Callus, score: 23.893	N	N	N	N
vg0817358920	A -> DEL	N	N	silent_mutation	Average:7.291; most accessible tissue: Callus, score: 23.893	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817358920	5.96E-06	NA	mr1051	Ind_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
vg0817358920	NA	2.43E-06	mr1229	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
vg0817358920	NA	2.15E-06	mr1351	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
vg0817358920	5.58E-06	7.74E-08	mr1523	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