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Detailed information for vg0819199007:

Variant ID: vg0819199007 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19199007
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACACATATACTACGTAGACCAAAACCACCGCGGATTTGGTCGAGAGGGGTAATTCGTCCGGTTTGCATAGTTGGTGGTGAAGAATGTCCGGTTTTGTG[G/A]
TTTAGGGGGTAATTCGGACAACTACGATAGTTCGGGGGAGGGTAATTCGTACTTTTTCCTATTTAGTATCATGGCATTGCATGATTTGAAGAGTACGCAT

Reverse complement sequence

ATGCGTACTCTTCAAATCATGCAATGCCATGATACTAAATAGGAAAAAGTACGAATTACCCTCCCCCGAACTATCGTAGTTGTCCGAATTACCCCCTAAA[C/T]
CACAAAACCGGACATTCTTCACCACCAACTATGCAAACCGGACGAATTACCCCTCTCGACCAAATCCGCGGTGGTTTTGGTCTACGTAGTATATGTGTGG

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	89.30%	8.40%	2.24%	0.00%	NA
All Indica	2759	98.20%	0.20%	1.56%	0.00%	NA
All Japonica	1512	70.80%	25.10%	4.03%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	96.10%	0.10%	3.83%	0.00%	NA
Indica Intermediate	786	99.00%	0.30%	0.76%	0.00%	NA
Temperate Japonica	767	85.00%	9.00%	6.00%	0.00%	NA
Tropical Japonica	504	43.50%	54.40%	2.18%	0.00%	NA
Japonica Intermediate	241	83.00%	15.40%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	14.40%	2.22%	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
vg0819199007	G -> A	LOC_Os08g31080-LOC_Os08g31090	intergenic_region ; MODIFIER	silent_mutation	Average:62.112; most accessible tissue: Callus, score: 91.803	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819199007	NA	1.36E-09	mr1097	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
vg0819199007	NA	1.88E-07	mr1206	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
vg0819199007	NA	1.84E-06	mr1773	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