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Detailed information for vg1200353257:

Variant ID: vg1200353257 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 353257
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, T: 0.15, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CCACTTGGTCTAGGAGTAAGTGGCGCTGCATTGGCAACAGTGACTTCTGAGTATGTTGAACTTACTGTGAGACTTTACAACAAATTTACCTTTTCTTTCA[A/T]
TTGTAGTCTCTTCACTTATCTCAATATTTTCTATAAGTTCTCATAGATCCCTGATCTATTTTTCATAATTATCTGCATGTATTTAGGTATTTGACAGCGT

Reverse complement sequence

ACGCTGTCAAATACCTAAATACATGCAGATAATTATGAAAAATAGATCAGGGATCTATGAGAACTTATAGAAAATATTGAGATAAGTGAAGAGACTACAA[T/A]
TGAAAGAAAAGGTAAATTTGTTGTAAAGTCTCACAGTAAGTTCAACATACTCAGAAGTCACTGTTGCCAATGCAGCGCCACTTACTCCTAGACCAAGTGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.80%	6.20%	0.00%	0.00%	NA
All Indica	2759	89.90%	10.10%	0.00%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.40%	9.60%	0.00%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	85.70%	14.30%	0.00%	0.00%	NA
Indica Intermediate	786	89.80%	10.20%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1200353257	A -> T	LOC_Os12g01574.1	upstream_gene_variant ; 2612.0bp to feature; MODIFIER	silent_mutation	Average:54.191; most accessible tissue: Callus, score: 77.663	N	N	N	N
vg1200353257	A -> T	LOC_Os12g01570.1	downstream_gene_variant ; 4112.0bp to feature; MODIFIER	silent_mutation	Average:54.191; most accessible tissue: Callus, score: 77.663	N	N	N	N
vg1200353257	A -> T	LOC_Os12g01590.1	downstream_gene_variant ; 2266.0bp to feature; MODIFIER	silent_mutation	Average:54.191; most accessible tissue: Callus, score: 77.663	N	N	N	N
vg1200353257	A -> T	LOC_Os12g01580.1	intron_variant ; MODIFIER	silent_mutation	Average:54.191; most accessible tissue: Callus, score: 77.663	N	N	N	N
vg1200353257	A -> T	LOC_Os12g01580.2	intron_variant ; MODIFIER	silent_mutation	Average:54.191; most accessible tissue: Callus, score: 77.663	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200353257	NA	1.09E-08	Awn_length	Ind_All	Not	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