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Detailed information for vg0922595826:

Variant ID: vg0922595826 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22595826
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CCCTTGTTCTTGTTAGGAAAGATAAAAACATGTGTTTTCCAATTGATTAGGGCACATACATATATACATATGCGTCGATCTAATAGGTTTAATATTCTTA[T/G]
CGATTACAACATGCAGGTTTGCTATTTGTGAAAGCAGGCAAGGTTATGATGGTTAGCATTGGAACGGATCACAGGGTTAGGGATGAATCAGCAGAACAAA

Reverse complement sequence

TTTGTTCTGCTGATTCATCCCTAACCCTGTGATCCGTTCCAATGCTAACCATCATAACCTTGCCTGCTTTCACAAATAGCAAACCTGCATGTTGTAATCG[A/C]
TAAGAATATTAAACCTATTAGATCGACGCATATGTATATATGTATGTGCCCTAATCAATTGGAAAACACATGTTTTTATCTTTCCTAACAAGAACAAGGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.00%	2.30%	2.41%	49.30%	NA
All Indica	2759	18.40%	3.20%	3.33%	74.99%	NA
All Japonica	1512	99.50%	0.00%	0.00%	0.53%	NA
Aus	269	5.90%	6.30%	6.69%	81.04%	NA
Indica I	595	33.10%	2.20%	2.18%	62.52%	NA
Indica II	465	10.10%	4.30%	3.01%	82.58%	NA
Indica III	913	8.90%	3.50%	3.72%	83.90%	NA
Indica Intermediate	786	23.40%	3.10%	3.94%	69.59%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.00%	0.00%	0.00%	0.99%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	89.60%	0.00%	1.04%	9.38%	NA
Intermediate	90	65.60%	2.20%	3.33%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0922595826	T -> G	LOC_Os09g39320.1	downstream_gene_variant ; 3148.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922595826	T -> G	LOC_Os09g39310.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922595826	T -> DEL	N	N	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
vg0922595826	2.85E-16	1.25E-75	mr1865	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
vg0922595826	9.32E-15	2.91E-18	mr1865	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
vg0922595826	1.28E-13	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
vg0922595826	3.89E-13	1.37E-15	mr1865_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