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Detailed information for vg0910969166:

Variant ID: vg0910969166 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10969166
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

ACGAGTGGTTTTGTGTGAAACTAGACTCAATAAGCTTTTCAAAAAGTGCTCATTCACCTTCATAGCTTTTGAGAATCAAAAGTTATGATGATTTCTTAAA[T/C]
TGGTCCGTTTTTCACTGTAACGGTTTGATCTTCATGGTCCGATTCAGCTTCCTCTTGTTGCATATTCTTAAGCACAACCAAAGTAGAACATTTTGGTAGT

Reverse complement sequence

ACTACCAAAATGTTCTACTTTGGTTGTGCTTAAGAATATGCAACAAGAGGAAGCTGAATCGGACCATGAAGATCAAACCGTTACAGTGAAAAACGGACCA[A/G]
TTTAAGAAATCATCATAACTTTTGATTCTCAAAAGCTATGAAGGTGAATGAGCACTTTTTGAAAAGCTTATTGAGTCTAGTTTCACACAAAACCACTCGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.10%	39.90%	2.56%	3.41%	NA
All Indica	2759	80.20%	17.60%	1.27%	0.94%	NA
All Japonica	1512	4.60%	83.40%	4.30%	7.67%	NA
Aus	269	82.50%	13.40%	3.72%	0.37%	NA
Indica I	595	57.00%	39.20%	1.85%	2.02%	NA
Indica II	465	81.50%	15.70%	1.51%	1.29%	NA
Indica III	913	96.10%	3.20%	0.55%	0.22%	NA
Indica Intermediate	786	78.60%	19.10%	1.53%	0.76%	NA
Temperate Japonica	767	3.00%	92.30%	1.56%	3.13%	NA
Tropical Japonica	504	5.00%	77.60%	5.75%	11.71%	NA
Japonica Intermediate	241	9.10%	67.20%	9.96%	13.69%	NA
VI/Aromatic	96	28.10%	56.20%	7.29%	8.33%	NA
Intermediate	90	30.00%	54.40%	4.44%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910969166	T -> DEL	N	N	silent_mutation	Average:25.0; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg0910969166	T -> C	LOC_Os09g17910.1	downstream_gene_variant ; 3665.0bp to feature; MODIFIER	silent_mutation	Average:25.0; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg0910969166	T -> C	LOC_Os09g17920.1	downstream_gene_variant ; 1504.0bp to feature; MODIFIER	silent_mutation	Average:25.0; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N
vg0910969166	T -> C	LOC_Os09g17910-LOC_Os09g17920	intergenic_region ; MODIFIER	silent_mutation	Average:25.0; most accessible tissue: Minghui63 root, score: 36.81	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910969166	4.15E-06	NA	mr1125_2	Jap_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