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Detailed information for vg1200352221:

Variant ID: vg1200352221 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 352221
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TCAGCTGATAATAAGGAATCAAAACAACAGTCCTTGATCAATGTGTGAATATGAAGCCAAACTAGAATTTACATTAAAATAATAGCATGACACTATAACA[A/G]
TATTTGGACAAAGTTTGTACCGTAAGCATATTACTTATTTATATGGATACCAGCATATTACAGAGCACAAAATATTTACCTAACGGGCCCTTGAAACTGA

Reverse complement sequence

TCAGTTTCAAGGGCCCGTTAGGTAAATATTTTGTGCTCTGTAATATGCTGGTATCCATATAAATAAGTAATATGCTTACGGTACAAACTTTGTCCAAATA[T/C]
TGTTATAGTGTCATGCTATTATTTTAATGTAAATTCTAGTTTGGCTTCATATTCACACATTGATCAAGGACTGTTGTTTTGATTCCTTATTATCAGCTGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.00%	6.00%	0.00%	0.00%	NA
All Indica	2759	90.00%	10.00%	0.00%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.60%	9.40%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg1200352221	A -> G	LOC_Os12g01574.1	upstream_gene_variant ; 1576.0bp to feature; MODIFIER	silent_mutation	Average:52.811; most accessible tissue: Callus, score: 81.076	N	N	N	N
vg1200352221	A -> G	LOC_Os12g01570.1	downstream_gene_variant ; 3076.0bp to feature; MODIFIER	silent_mutation	Average:52.811; most accessible tissue: Callus, score: 81.076	N	N	N	N
vg1200352221	A -> G	LOC_Os12g01590.1	downstream_gene_variant ; 3302.0bp to feature; MODIFIER	silent_mutation	Average:52.811; most accessible tissue: Callus, score: 81.076	N	N	N	N
vg1200352221	A -> G	LOC_Os12g01580.1	intron_variant ; MODIFIER	silent_mutation	Average:52.811; most accessible tissue: Callus, score: 81.076	N	N	N	N
vg1200352221	A -> G	LOC_Os12g01580.2	intron_variant ; MODIFIER	silent_mutation	Average:52.811; most accessible tissue: Callus, score: 81.076	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200352221	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