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Detailed information for vg0136606599:

Variant ID: vg0136606599 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 36606599
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAAATATGGTAAGAACTGCAAGTACTACATGCATGTCCATCTACCAAAAATACAACAATAACCATGATTTGACTTGATTACACCTTAATATATAAAAA[T/A]
TGACTCCAAAAGTTTCATCTCACTAATTTACATTATCCTAATCTGTTAAGCTGGTGGAACAGACCGCGCTAAGGTGTCACTGCTTTGCAAACCACTTTTC

Reverse complement sequence

GAAAAGTGGTTTGCAAAGCAGTGACACCTTAGCGCGGTCTGTTCCACCAGCTTAACAGATTAGGATAATGTAAATTAGTGAGATGAAACTTTTGGAGTCA[A/T]
TTTTTATATATTAAGGTGTAATCAAGTCAAATCATGGTTATTGTTGTATTTTTGGTAGATGGACATGCATGTAGTACTTGCAGTTCTTACCATATTTTAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.70%	3.10%	0.23%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	89.70%	9.50%	0.73%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	84.40%	14.30%	1.30%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	88.80%	10.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0136606599	T -> A	LOC_Os01g63160.1	3_prime_UTR_variant ; 46.0bp to feature; MODIFIER	silent_mutation	Average:49.71; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0136606599	T -> A	LOC_Os01g63170.1	upstream_gene_variant ; 4178.0bp to feature; MODIFIER	silent_mutation	Average:49.71; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0136606599	6.90E-20	2.22E-26	Awn_length	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
vg0136606599	1.52E-09	2.11E-14	Awn_length	Jap_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