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Detailed information for vg0909282800:

Variant ID: vg0909282800 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9282800
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.03, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

AATGATAGGAAAAGAATTAATAATTGCTTAAATTTTTTAAATAAGACGAACGGTCAAACATGTGCTAAAAAGTCAATGGCGTCAAACATTTCAAAACGAA[G/T]
GGAGTATTTCTTTAGCATAGTTTGATGCATGTTTCTTCAGATCAGGTCAAAAAGAAAGGACCATCAAACAGAGCTGCCAGAGTAATGTAAGGCCATATGA

Reverse complement sequence

TCATATGGCCTTACATTACTCTGGCAGCTCTGTTTGATGGTCCTTTCTTTTTGACCTGATCTGAAGAAACATGCATCAAACTATGCTAAAGAAATACTCC[C/A]
TTCGTTTTGAAATGTTTGACGCCATTGACTTTTTAGCACATGTTTGACCGTTCGTCTTATTTAAAAAATTTAAGCAATTATTAATTCTTTTCCTATCATT

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	57.50%	40.90%	0.25%	1.33%	NA
All Indica	2759	31.00%	68.60%	0.33%	0.04%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.07%	NA
Aus	269	98.50%	0.70%	0.00%	0.74%	NA
Indica I	595	25.50%	73.90%	0.50%	0.00%	NA
Indica II	465	20.20%	79.60%	0.22%	0.00%	NA
Indica III	913	40.20%	59.60%	0.22%	0.00%	NA
Indica Intermediate	786	30.80%	68.70%	0.38%	0.13%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	41.70%	2.10%	1.04%	55.21%	NA
Intermediate	90	64.40%	26.70%	2.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909282800	G -> DEL	N	N	silent_mutation	Average:29.221; most accessible tissue: Callus, score: 45.947	N	N	N	N
vg0909282800	G -> T	LOC_Os09g15260.1	upstream_gene_variant ; 677.0bp to feature; MODIFIER	silent_mutation	Average:29.221; most accessible tissue: Callus, score: 45.947	N	N	N	N
vg0909282800	G -> T	LOC_Os09g15250-LOC_Os09g15260	intergenic_region ; MODIFIER	silent_mutation	Average:29.221; most accessible tissue: Callus, score: 45.947	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909282800	NA	1.05E-09	mr1220_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
vg0909282800	NA	1.29E-07	mr1302_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
vg0909282800	NA	1.55E-08	mr1319_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
vg0909282800	NA	3.63E-07	mr1346_2	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
vg0909282800	NA	4.75E-14	mr1579_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
vg0909282800	NA	7.66E-07	mr1824_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
vg0909282800	NA	2.45E-06	mr1834_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