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Detailed information for vg0922436617:

Variant ID: vg0922436617 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22436617
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTTAATGGGATACACGCCGTACATGGATATGCCACATAGCCCTTCCTTAGCTGCTATGTCACGCTTCATGCGGATGTAGCCACTCTCTCCCCATCTAG[G/T]
ACCCCACGAGTTCCTAGCAATCCAATAGTTGATGTTGTCCTGTGTCACGCCATACCCAACAGTTGTTACTGCATGGTTTACCGATGTCCCGCACGGTCCA

Reverse complement sequence

TGGACCGTGCGGGACATCGGTAAACCATGCAGTAACAACTGTTGGGTATGGCGTGACACAGGACAACATCAACTATTGGATTGCTAGGAACTCGTGGGGT[C/A]
CTAGATGGGGAGAGAGTGGCTACATCCGCATGAAGCGTGACATAGCAGCTAAGGAAGGGCTATGTGGCATATCCATGTACGGCGTGTATCCCATTAAGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.80%	31.80%	4.36%	22.05%	NA
All Indica	2759	5.40%	52.20%	6.96%	35.45%	NA
All Japonica	1512	99.60%	0.30%	0.07%	0.00%	NA
Aus	269	64.30%	14.50%	2.97%	18.22%	NA
Indica I	595	2.90%	46.60%	13.28%	37.31%	NA
Indica II	465	4.70%	59.60%	7.96%	27.74%	NA
Indica III	913	5.40%	54.40%	2.08%	38.12%	NA
Indica Intermediate	786	7.80%	49.50%	7.25%	35.50%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	93.80%	2.10%	2.08%	2.08%	NA
Intermediate	90	64.40%	17.80%	3.33%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0922436617	G -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922436617	G -> T	LOC_Os09g39080.1	upstream_gene_variant ; 2941.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922436617	G -> T	LOC_Os09g39090.1	downstream_gene_variant ; 1442.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922436617	G -> T	LOC_Os09g39080-LOC_Os09g39090	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
vg0922436617	6.97E-21	NA	mr1865	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
vg0922436617	6.48E-20	8.51E-24	mr1865	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
vg0922436617	3.12E-18	NA	mr1865_2	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
vg0922436617	2.13E-16	1.40E-23	mr1865_2	Ind_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
vg0922436617	NA	2.43E-06	mr1925_2	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