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Detailed information for vg0818919268:

Variant ID: vg0818919268 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18919268
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTAACTTCAAAAAGTTTTCAAATCTAGGTTGAAAGTTTTTAAATTTAGGTTGAATGTTTTCAAATCTGGATTGAAAGTTTTCAGAATTTGACTTCA[C/T]
GTATAGATTTCTTTTCAATCTATTACTTAAAATAATCTTCGGAAAAAAGACAAATCTTATCTTAACCGAATCAGTTTTGAATCAGTTTTATAGAGAAAAA

Reverse complement sequence

TTTTTCTCTATAAAACTGATTCAAAACTGATTCGGTTAAGATAAGATTTGTCTTTTTTCCGAAGATTATTTTAAGTAATAGATTGAAAAGAAATCTATAC[G/A]
TGAAGTCAAATTCTGAAAACTTTCAATCCAGATTTGAAAACATTCAACCTAAATTTAAAAACTTTCAACCTAGATTTGAAAACTTTTTGAAGTTAAATTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.30%	38.00%	0.47%	20.19%	NA
All Indica	2759	63.90%	8.20%	0.58%	27.40%	NA
All Japonica	1512	1.50%	86.40%	0.07%	12.10%	NA
Aus	269	49.80%	49.10%	0.00%	1.12%	NA
Indica I	595	77.80%	16.10%	0.34%	5.71%	NA
Indica II	465	87.50%	4.10%	0.22%	8.17%	NA
Indica III	913	46.50%	5.40%	0.66%	47.43%	NA
Indica Intermediate	786	59.40%	7.80%	0.89%	31.93%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	64.10%	0.20%	33.33%	NA
Japonica Intermediate	241	1.70%	92.10%	0.00%	6.22%	NA
VI/Aromatic	96	3.10%	90.60%	0.00%	6.25%	NA
Intermediate	90	34.40%	53.30%	5.56%	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
vg0818919268	C -> T	LOC_Os08g30680.1	downstream_gene_variant ; 2949.0bp to feature; MODIFIER	silent_mutation	Average:34.863; most accessible tissue: Callus, score: 55.146	N	N	N	N
vg0818919268	C -> T	LOC_Os08g30670-LOC_Os08g30680	intergenic_region ; MODIFIER	silent_mutation	Average:34.863; most accessible tissue: Callus, score: 55.146	N	N	N	N
vg0818919268	C -> DEL	N	N	silent_mutation	Average:34.863; most accessible tissue: Callus, score: 55.146	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818919268	NA	5.70E-06	mr1705	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