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Detailed information for vg0727324847:

Variant ID: vg0727324847 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27324847
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, T: 0.17, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

CTGATCCTGTCTCAACTGTGAACTGTTGTTGCTGAGGCAGATGCTGAGGCTGTTTTGCTTTTGAGGAGGGTGACCTGTGGCTCTTTTCCTTGTTATCTTT[A/T]
ACAAGGTTAATTGAGCCACCAATGGTCTCTTTGATTCTTTCCTCCTCTTGCACACAATTAGAGATGAGCTCTTCAATATTCCATTTCTCTGGACTTATTT

Reverse complement sequence

AAATAAGTCCAGAGAAATGGAATATTGAAGAGCTCATCTCTAATTGTGTGCAAGAGGAGGAAAGAATCAAAGAGACCATTGGTGGCTCAATTAACCTTGT[T/A]
AAAGATAACAAGGAAAAGAGCCACAGGTCACCCTCCTCAAAAGCAAAACAGCCTCAGCATCTGCCTCAGCAACAACAGTTCACAGTTGAGACAGGATCAG

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	48.10%	24.70%	3.43%	23.74%	NA
All Indica	2759	26.60%	33.70%	4.68%	35.01%	NA
All Japonica	1512	92.90%	6.00%	0.07%	1.06%	NA
Aus	269	23.40%	47.20%	10.41%	18.96%	NA
Indica I	595	32.80%	47.20%	4.20%	15.80%	NA
Indica II	465	28.20%	14.20%	6.45%	51.18%	NA
Indica III	913	12.00%	42.70%	4.16%	41.07%	NA
Indica Intermediate	786	37.80%	24.70%	4.58%	32.95%	NA
Temperate Japonica	767	95.40%	3.80%	0.00%	0.78%	NA
Tropical Japonica	504	87.50%	11.10%	0.20%	1.19%	NA
Japonica Intermediate	241	95.90%	2.50%	0.00%	1.66%	NA
VI/Aromatic	96	15.60%	6.20%	2.08%	76.04%	NA
Intermediate	90	65.60%	14.40%	2.22%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0727324847	A -> DEL	LOC_Os07g45770.1	N	frameshift_variant	Average:6.312; most accessible tissue: Callus, score: 15.876	N	N	N	N
vg0727324847	A -> T	LOC_Os07g45770.1	synonymous_variant ; p.Val292Val; LOW	synonymous_codon	Average:6.312; most accessible tissue: Callus, score: 15.876	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727324847	2.40E-06	5.78E-06	mr1875	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
vg0727324847	6.78E-06	6.78E-06	mr1875	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0727324847	9.66E-06	NA	mr1908	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251