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Detailed information for vg0900106167:

Variant ID: vg0900106167 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 106167
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCAGCAAGTTATCACGGAAATATGTTATGCATTGACATATAATAGGGTTCTTTGCAAAAAGCAGTATTGGACAATCTGGAAAAATTATAGCTGAATTT[G/A]
TAAACATATAAACTTTAGATTCCTAACCAGGGTACCATATGAGTCCCGGTACTCAACTCCATGAGTACGGCTATTCGAATAGTTTCAAAGATATTCTACT

Reverse complement sequence

AGTAGAATATCTTTGAAACTATTCGAATAGCCGTACTCATGGAGTTGAGTACCGGGACTCATATGGTACCCTGGTTAGGAATCTAAAGTTTATATGTTTA[C/T]
AAATTCAGCTATAATTTTTCCAGATTGTCCAATACTGCTTTTTGCAAAGAACCCTATTATATGTCAATGCATAACATATTTCCGTGATAACTTGCTGAGT

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	66.20%	1.00%	6.69%	26.15%	NA
All Indica	2759	53.90%	1.10%	9.57%	35.48%	NA
All Japonica	1512	88.40%	0.50%	0.26%	10.85%	NA
Aus	269	64.30%	0.70%	9.29%	25.65%	NA
Indica I	595	74.30%	0.00%	4.87%	20.84%	NA
Indica II	465	60.00%	5.20%	10.11%	24.73%	NA
Indica III	913	36.70%	0.40%	13.58%	49.29%	NA
Indica Intermediate	786	54.70%	0.30%	8.14%	36.90%	NA
Temperate Japonica	767	83.80%	0.50%	0.39%	15.25%	NA
Tropical Japonica	504	91.50%	0.20%	0.20%	8.13%	NA
Japonica Intermediate	241	96.30%	1.20%	0.00%	2.49%	NA
VI/Aromatic	96	65.60%	5.20%	19.79%	9.38%	NA
Intermediate	90	77.80%	1.10%	4.44%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900106167	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900106167	G -> A	LOC_Os09g01080.1	upstream_gene_variant ; 3177.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900106167	G -> A	LOC_Os09g01090.1	upstream_gene_variant ; 2386.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900106167	G -> A	LOC_Os09g01090-LOC_Os09g01100	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900106167	5.39E-06	NA	mr1996_2	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