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Detailed information for vg0909586409:

Variant ID: vg0909586409 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9586409
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAGGTACTTCCAATATTTGAATTTTATTGAAAAACTAGAAAGGAAGCCCGTACATATGCACGGGCATATCGTATTTATTGCTAAGAGAATTAAGTCATA[T/A]
CTCACCATATACATATAAGAATAGATTTGGCCTCGTAATAAAAAAAATATGTTGTAAAATAGACCGTAGACTTTTATATAAATGATAAGCATGTCTCTTA

Reverse complement sequence

TAAGAGACATGCTTATCATTTATATAAAAGTCTACGGTCTATTTTACAACATATTTTTTTTATTACGAGGCCAAATCTATTCTTATATGTATATGGTGAG[A/T]
TATGACTTAATTCTCTTAGCAATAAATACGATATGCCCGTGCATATGTACGGGCTTCCTTTCTAGTTTTTCAATAAAATTCAAATATTGGAAGTACCTGG

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	79.80%	3.00%	0.68%	16.44%	NA
All Indica	2759	83.00%	0.10%	0.18%	16.78%	NA
All Japonica	1512	76.30%	9.30%	1.52%	12.90%	NA
Aus	269	75.80%	0.00%	0.37%	23.79%	NA
Indica I	595	86.70%	0.00%	0.00%	13.28%	NA
Indica II	465	82.80%	0.00%	0.00%	17.20%	NA
Indica III	913	80.60%	0.00%	0.22%	19.17%	NA
Indica Intermediate	786	83.00%	0.30%	0.38%	16.41%	NA
Temperate Japonica	767	76.50%	8.50%	0.39%	14.60%	NA
Tropical Japonica	504	76.60%	11.30%	3.77%	8.33%	NA
Japonica Intermediate	241	74.70%	7.90%	0.41%	17.01%	NA
VI/Aromatic	96	50.00%	0.00%	3.12%	46.88%	NA
Intermediate	90	87.80%	1.10%	0.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909586409	T -> DEL	N	N	silent_mutation	Average:39.2; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0909586409	T -> A	LOC_Os09g15710.1	upstream_gene_variant ; 2797.0bp to feature; MODIFIER	silent_mutation	Average:39.2; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0909586409	T -> A	LOC_Os09g15700-LOC_Os09g15710	intergenic_region ; MODIFIER	silent_mutation	Average:39.2; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909586409	4.84E-08	NA	Awn_length	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
vg0909586409	NA	1.03E-07	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
vg0909586409	2.46E-08	NA	mr1549_2	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