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Detailed information for vg1108744582:

Variant ID: vg1108744582 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8744582
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGTGCCTAAACCGGGGCTGGGAAAACCTCCGAGGCCTCCTAAGAGGAAGGTGACTGATAAGGCGGATGATCCAGAGATGCAAAAGGAAAATCCAGTGCC[A/G]
GAAGTGCCACCGGAGATTGCATTGCCGAAGGCAGCCATGGAGATTGCACCGCCGGAGATAGCCTTGGAGATTCCAGTGCCAGATGTGCCCATGGAGATTA

Reverse complement sequence

TAATCTCCATGGGCACATCTGGCACTGGAATCTCCAAGGCTATCTCCGGCGGTGCAATCTCCATGGCTGCCTTCGGCAATGCAATCTCCGGTGGCACTTC[T/C]
GGCACTGGATTTTCCTTTTGCATCTCTGGATCATCCGCCTTATCAGTCACCTTCCTCTTAGGAGGCCTCGGAGGTTTTCCCAGCCCCGGTTTAGGCACCA

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	65.40%	4.60%	11.51%	18.47%	NA
All Indica	2759	46.00%	6.80%	18.27%	28.89%	NA
All Japonica	1512	95.20%	1.30%	0.79%	2.65%	NA
Aus	269	85.50%	1.90%	4.83%	7.81%	NA
Indica I	595	36.10%	5.00%	22.69%	36.13%	NA
Indica II	465	51.20%	0.90%	20.22%	27.74%	NA
Indica III	913	46.10%	11.30%	16.87%	25.74%	NA
Indica Intermediate	786	50.40%	6.50%	15.39%	27.74%	NA
Temperate Japonica	767	98.40%	0.00%	0.52%	1.04%	NA
Tropical Japonica	504	93.10%	4.00%	0.99%	1.98%	NA
Japonica Intermediate	241	89.60%	0.00%	1.24%	9.13%	NA
VI/Aromatic	96	93.80%	0.00%	5.21%	1.04%	NA
Intermediate	90	67.80%	5.60%	11.11%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108744582	A -> DEL	LOC_Os11g15430.1	N	frameshift_variant	Average:12.631; most accessible tissue: Callus, score: 32.201	N	N	N	N
vg1108744582	A -> G	LOC_Os11g15430.1	synonymous_variant ; p.Pro389Pro; LOW	synonymous_codon	Average:12.631; most accessible tissue: Callus, score: 32.201	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108744582	NA	2.16E-06	mr1672	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