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Detailed information for vg0804040328:

Variant ID: vg0804040328 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4040328
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCTTACCCTTGCTGCTGGGGAGTGGGTATATATACCCCCAACAACCAAAACTAGCCGTTGGAGTCGAAATACCCAACTCTGTGCTCCGCCGGTCAGACC[G/A]
CCATAGAGTGGCCGGTCAGACCGGACTACTATGTAACGGCTAGAAAACTAGCCATTACAGGGCAATCATTGAGCCCACTCAACCTGGCCGGTCTGACCGC

Reverse complement sequence

GCGGTCAGACCGGCCAGGTTGAGTGGGCTCAATGATTGCCCTGTAATGGCTAGTTTTCTAGCCGTTACATAGTAGTCCGGTCTGACCGGCCACTCTATGG[C/T]
GGTCTGACCGGCGGAGCACAGAGTTGGGTATTTCGACTCCAACGGCTAGTTTTGGTTGTTGGGGGTATATATACCCACTCCCCAGCAGCAAGGGTAAGGT

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	61.90%	12.00%	26.13%	0.04%	NA
All Indica	2759	39.80%	20.20%	40.09%	0.00%	NA
All Japonica	1512	98.60%	0.10%	1.19%	0.13%	NA
Aus	269	72.90%	0.70%	26.39%	0.00%	NA
Indica I	595	21.50%	17.50%	61.01%	0.00%	NA
Indica II	465	83.20%	2.60%	14.19%	0.00%	NA
Indica III	913	29.80%	33.60%	36.58%	0.00%	NA
Indica Intermediate	786	39.40%	16.90%	43.64%	0.00%	NA
Temperate Japonica	767	98.00%	0.00%	1.69%	0.26%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	80.20%	1.00%	18.75%	0.00%	NA
Intermediate	90	70.00%	5.60%	24.44%	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
vg0804040328	G -> A	LOC_Os08g07240.1	upstream_gene_variant ; 1247.0bp to feature; MODIFIER	silent_mutation	Average:29.199; most accessible tissue: Minghui63 flag leaf, score: 59.912	N	N	N	N
vg0804040328	G -> A	LOC_Os08g07240-LOC_Os08g07260	intergenic_region ; MODIFIER	silent_mutation	Average:29.199; most accessible tissue: Minghui63 flag leaf, score: 59.912	N	N	N	N
vg0804040328	G -> DEL	N	N	silent_mutation	Average:29.199; most accessible tissue: Minghui63 flag leaf, score: 59.912	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804040328	NA	9.19E-06	mr1296	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
vg0804040328	2.55E-06	2.55E-06	mr1296	Ind_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
vg0804040328	NA	9.49E-07	mr1717	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