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Detailed information for vg0911407067:

Variant ID: vg0911407067 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11407067
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

CCGTCGTGCCATCCTGTCTTGTTTTGCAATTGAAACTTCCTTAGCTCCTTTTCCCCTTTTGCTTCTTCTATTCATTGCTTCTTCCACTGAATGTCTGTGA[T/A]
ATAGAGAGAACAAAAAACCAGGGGAAAAGGGTATAATCAGTCCGTGATCGAGACGCCGCTTTGACCCCATCCCCCCTCGGGCTCGTTCTAGCGAGACGGT

Reverse complement sequence

ACCGTCTCGCTAGAACGAGCCCGAGGGGGGATGGGGTCAAAGCGGCGTCTCGATCACGGACTGATTATACCCTTTTCCCCTGGTTTTTTGTTCTCTCTAT[A/T]
TCACAGACATTCAGTGGAAGAAGCAATGAATAGAAGAAGCAAAAGGGGAAAAGGAGCTAAGGAAGTTTCAATTGCAAAACAAGACAGGATGGCACGACGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.10%	17.10%	1.21%	48.60%	NA
All Indica	2759	13.80%	28.60%	1.74%	55.89%	NA
All Japonica	1512	73.30%	0.50%	0.07%	26.12%	NA
Aus	269	8.60%	1.50%	0.74%	89.22%	NA
Indica I	595	13.80%	14.10%	2.35%	69.75%	NA
Indica II	465	8.00%	44.30%	0.86%	46.88%	NA
Indica III	913	16.40%	25.30%	2.41%	55.86%	NA
Indica Intermediate	786	14.10%	34.10%	1.02%	50.76%	NA
Temperate Japonica	767	66.50%	0.50%	0.13%	32.86%	NA
Tropical Japonica	504	85.70%	0.20%	0.00%	14.09%	NA
Japonica Intermediate	241	69.30%	0.80%	0.00%	29.88%	NA
VI/Aromatic	96	9.40%	3.10%	6.25%	81.25%	NA
Intermediate	90	48.90%	4.40%	0.00%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911407067	T -> DEL	N	N	silent_mutation	Average:39.277; most accessible tissue: Minghui63 root, score: 79.954	N	N	N	N
vg0911407067	T -> A	LOC_Os09g18620.1	upstream_gene_variant ; 4839.0bp to feature; MODIFIER	silent_mutation	Average:39.277; most accessible tissue: Minghui63 root, score: 79.954	N	N	N	N
vg0911407067	T -> A	LOC_Os09g18610.1	downstream_gene_variant ; 210.0bp to feature; MODIFIER	silent_mutation	Average:39.277; most accessible tissue: Minghui63 root, score: 79.954	N	N	N	N
vg0911407067	T -> A	LOC_Os09g18610-LOC_Os09g18620	intergenic_region ; MODIFIER	silent_mutation	Average:39.277; most accessible tissue: Minghui63 root, score: 79.954	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911407067	6.84E-06	NA	mr1754	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