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Detailed information for vg0817041494:

Variant ID: vg0817041494 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17041494
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTCAGCTCTATCTCCTATCTCTCTTCTCATCTCTCTCTCTATATTCTCTCTCAGAGGAGCATGTGGCGGCGTCGGTCGCCAGGGCTTGAGCTCGTCGC[A/G]
GCGGAGGAGATGGTGAGGACGGCGGCTGGTAGAGTGGAGCAAGGCGTCAGCTGCGGTGGAGCGGAGCTTGCGGCCGACCGAAGCAGGTGGGCAAGCACGC

Reverse complement sequence

GCGTGCTTGCCCACCTGCTTCGGTCGGCCGCAAGCTCCGCTCCACCGCAGCTGACGCCTTGCTCCACTCTACCAGCCGCCGTCCTCACCATCTCCTCCGC[T/C]
GCGACGAGCTCAAGCCCTGGCGACCGACGCCGCCACATGCTCCTCTGAGAGAGAATATAGAGAGAGAGATGAGAAGAGAGATAGGAGATAGAGCTGACAT

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	51.60%	46.50%	1.31%	0.57%	NA
All Indica	2759	46.40%	51.80%	0.94%	0.87%	NA
All Japonica	1512	51.10%	48.00%	0.73%	0.13%	NA
Aus	269	90.30%	1.10%	8.55%	0.00%	NA
Indica I	595	71.60%	27.70%	0.67%	0.00%	NA
Indica II	465	14.60%	81.50%	0.22%	3.66%	NA
Indica III	913	47.40%	51.00%	1.31%	0.22%	NA
Indica Intermediate	786	44.90%	53.30%	1.15%	0.64%	NA
Temperate Japonica	767	28.90%	71.10%	0.00%	0.00%	NA
Tropical Japonica	504	79.40%	18.10%	2.18%	0.40%	NA
Japonica Intermediate	241	62.70%	37.30%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	54.40%	42.20%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817041494	A -> G	LOC_Os08g27960.1	downstream_gene_variant ; 4497.0bp to feature; MODIFIER	silent_mutation	Average:59.42; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0817041494	A -> G	LOC_Os08g27970.1	downstream_gene_variant ; 1706.0bp to feature; MODIFIER	silent_mutation	Average:59.42; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0817041494	A -> G	LOC_Os08g27970-LOC_Os08g27980	intergenic_region ; MODIFIER	silent_mutation	Average:59.42; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0817041494	A -> DEL	N	N	silent_mutation	Average:59.42; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817041494	NA	6.55E-08	mr1942	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
vg0817041494	NA	9.07E-06	mr1159_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
vg0817041494	5.29E-08	5.29E-08	mr1983_2	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