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Detailed information for vg0808223949:

Variant ID: vg0808223949 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8223949
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTTTGTAAGCTGAAAATCCCAGCCAGTTTAGCTTGCTTCCAGTTTACTCCCTTCGTCCTATAATGTAGCAACCTATTATGGTTACTACATTATGGGATA[G/A]
GTTGCTATATTATGGGACGGAGGGAGTATCTTTTTGTAAAGACTCTGTGTGTGTTGTGTGTTTAGGCTATCTCCAGAAGCCGGGTCAATATATTTGATCT

Reverse complement sequence

AGATCAAATATATTGACCCGGCTTCTGGAGATAGCCTAAACACACAACACACACAGAGTCTTTACAAAAAGATACTCCCTCCGTCCCATAATATAGCAAC[C/T]
TATCCCATAATGTAGTAACCATAATAGGTTGCTACATTATAGGACGAAGGGAGTAAACTGGAAGCAAGCTAAACTGGCTGGGATTTTCAGCTTACAAACA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.90%	0.40%	11.11%	24.57%	NA
All Indica	2759	47.60%	0.00%	17.22%	35.23%	NA
All Japonica	1512	89.10%	1.40%	1.98%	7.54%	NA
Aus	269	80.70%	0.00%	1.86%	17.47%	NA
Indica I	595	38.70%	0.00%	30.76%	30.59%	NA
Indica II	465	58.50%	0.00%	10.97%	30.54%	NA
Indica III	913	48.30%	0.00%	10.51%	41.18%	NA
Indica Intermediate	786	46.90%	0.00%	18.45%	34.61%	NA
Temperate Japonica	767	90.70%	2.70%	2.74%	3.78%	NA
Tropical Japonica	504	95.20%	0.00%	0.99%	3.77%	NA
Japonica Intermediate	241	71.00%	0.00%	1.66%	27.39%	NA
VI/Aromatic	96	87.50%	0.00%	8.33%	4.17%	NA
Intermediate	90	65.60%	0.00%	7.78%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808223949	G -> A	LOC_Os08g13790.1	upstream_gene_variant ; 3192.0bp to feature; MODIFIER	silent_mutation	Average:59.456; most accessible tissue: Callus, score: 94.996	N	N	N	N
vg0808223949	G -> A	LOC_Os08g13780.1	downstream_gene_variant ; 4902.0bp to feature; MODIFIER	silent_mutation	Average:59.456; most accessible tissue: Callus, score: 94.996	N	N	N	N
vg0808223949	G -> A	LOC_Os08g13795.1	downstream_gene_variant ; 206.0bp to feature; MODIFIER	silent_mutation	Average:59.456; most accessible tissue: Callus, score: 94.996	N	N	N	N
vg0808223949	G -> A	LOC_Os08g13790-LOC_Os08g13795	intergenic_region ; MODIFIER	silent_mutation	Average:59.456; most accessible tissue: Callus, score: 94.996	N	N	N	N
vg0808223949	G -> DEL	N	N	silent_mutation	Average:59.456; most accessible tissue: Callus, score: 94.996	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808223949	4.93E-09	4.82E-15	Awn_length	Jap_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0808223949	NA	7.74E-06	mr1274	Jap_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