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Detailed information for vg0916036409:

Variant ID: vg0916036409 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 16036409
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

TGTATTCAAATTTTAGTTTATGAAATTTGTTCGGAATTTACCGGTTTTCCACCGGATTTCGCGAAATTTCGAATTCCGCCAGTGCCCGAAACGGAAGGGC[C/A]
TATCGGAATCGTAAACCCTGCTGCTGTCTGCTGTTTGTTCTCTGCAGTTATCTTCAGTGCATGTGCATAAAAAAATAGCAGGTTATGTCTAGTGGCAATA

Reverse complement sequence

TATTGCCACTAGACATAACCTGCTATTTTTTTATGCACATGCACTGAAGATAACTGCAGAGAACAAACAGCAGACAGCAGCAGGGTTTACGATTCCGATA[G/T]
GCCCTTCCGTTTCGGGCACTGGCGGAATTCGAAATTTCGCGAAATCCGGTGGAAAACCGGTAAATTCCGAACAAATTTCATAAACTAAAATTTGAATACA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.10%	0.90%	11.96%	19.04%	NA
All Indica	2759	50.90%	1.20%	18.27%	29.65%	NA
All Japonica	1512	99.70%	0.00%	0.13%	0.20%	NA
Aus	269	50.90%	4.10%	19.70%	25.28%	NA
Indica I	595	55.10%	0.30%	18.49%	26.05%	NA
Indica II	465	39.40%	0.90%	20.22%	39.57%	NA
Indica III	913	54.30%	1.50%	17.20%	26.94%	NA
Indica Intermediate	786	50.60%	1.50%	18.19%	29.64%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	99.60%	0.00%	0.20%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	0.00%	6.67%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0916036409	C -> DEL	N	N	silent_mutation	Average:27.378; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0916036409	C -> A	LOC_Os09g26530.1	upstream_gene_variant ; 1054.0bp to feature; MODIFIER	silent_mutation	Average:27.378; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0916036409	C -> A	LOC_Os09g26540.1	downstream_gene_variant ; 2433.0bp to feature; MODIFIER	silent_mutation	Average:27.378; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0916036409	C -> A	LOC_Os09g26540.2	downstream_gene_variant ; 2433.0bp to feature; MODIFIER	silent_mutation	Average:27.378; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg0916036409	C -> A	LOC_Os09g26530-LOC_Os09g26540	intergenic_region ; MODIFIER	silent_mutation	Average:27.378; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0916036409	NA	3.24E-06	mr1374	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