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Detailed information for vg0807119511:

Variant ID: vg0807119511 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7119511
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTTCTACAACGGGCCAGAGCGGAAGGTGAGTAGCAGCGCATCCTCCGTGCTGCCAACGCCAGAGGCTCCCTCCTCCTGAGGAACCGAGGGCACGGGCTC[A/G]
GTGCGAGGGGTCTCGACAAAGCAGGTCTATGCCAAGGACTGACGAACAAGCTCGGGCCTGGAGGTACTCTTGCGGGCGGTGATCTTCAGGCTGCGGCAGA

Reverse complement sequence

TCTGCCGCAGCCTGAAGATCACCGCCCGCAAGAGTACCTCCAGGCCCGAGCTTGTTCGTCAGTCCTTGGCATAGACCTGCTTTGTCGAGACCCCTCGCAC[T/C]
GAGCCCGTGCCCTCGGTTCCTCAGGAGGAGGGAGCCTCTGGCGTTGGCAGCACGGAGGATGCGCTGCTACTCACCTTCCGCTCTGGCCCGTTGTAGAAGT

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	47.40%	11.60%	15.72%	25.31%	NA
All Indica	2759	38.30%	1.60%	19.97%	40.09%	NA
All Japonica	1512	53.70%	32.90%	10.45%	2.98%	NA
Aus	269	84.80%	0.70%	4.46%	10.04%	NA
Indica I	595	13.10%	3.50%	29.08%	54.29%	NA
Indica II	465	53.80%	1.10%	17.42%	27.74%	NA
Indica III	913	41.70%	0.20%	16.98%	41.07%	NA
Indica Intermediate	786	44.40%	2.00%	18.07%	35.50%	NA
Temperate Japonica	767	32.70%	48.20%	13.82%	5.22%	NA
Tropical Japonica	504	83.10%	11.10%	5.16%	0.60%	NA
Japonica Intermediate	241	58.90%	29.50%	10.79%	0.83%	NA
VI/Aromatic	96	89.60%	1.00%	5.21%	4.17%	NA
Intermediate	90	60.00%	5.60%	18.89%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0807119511	A -> G	LOC_Os08g12090.1	downstream_gene_variant ; 2710.0bp to feature; MODIFIER	silent_mutation	Average:28.737; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N
vg0807119511	A -> G	LOC_Os08g12080.1	intron_variant ; MODIFIER	silent_mutation	Average:28.737; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N
vg0807119511	A -> DEL	N	N	silent_mutation	Average:28.737; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807119511	6.90E-07	1.05E-08	mr1917	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