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Detailed information for vg0727206096:

Variant ID: vg0727206096 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27206096
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACGATACAAGATTAGACGAGATGATCCAGGTGAAGTTGACGGGCAGCCAACGAAGAAGAGAATTCCTGCTAAGGTGATGTGGTATTTCCCTATAATACC[A/T]
CGGTTAAGGCGTTTGTTCAGGAACAAGGGGAATGCTAGAATGATGCGTTGGCACGCTGAAGAACGTCAACAGGACGGGATGCTGAGACACCCCGCCGATG

Reverse complement sequence

CATCGGCGGGGTGTCTCAGCATCCCGTCCTGTTGACGTTCTTCAGCGTGCCAACGCATCATTCTAGCATTCCCCTTGTTCCTGAACAAACGCCTTAACCG[T/A]
GGTATTATAGGGAAATACCACATCACCTTAGCAGGAATTCTCTTCTTCGTTGGCTGCCCGTCAACTTCACCTGGATCATCTCGTCTAATCTTGTATCGTA

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	91.70%	3.60%	4.74%	0.00%	NA
All Indica	2759	89.00%	5.10%	5.87%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	84.80%	3.30%	11.90%	0.00%	NA
Indica I	595	96.30%	2.00%	1.68%	0.00%	NA
Indica II	465	80.40%	10.50%	9.03%	0.00%	NA
Indica III	913	88.80%	4.60%	6.57%	0.00%	NA
Indica Intermediate	786	88.70%	5.00%	6.36%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	54.20%	17.70%	28.12%	0.00%	NA
Intermediate	90	97.80%	0.00%	2.22%	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
vg0727206096	A -> T	LOC_Os07g45580.1	synonymous_variant ; p.Pro226Pro; LOW	synonymous_codon	Average:10.167; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727206096	NA	1.94E-06	mr1115_2	Ind_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