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Detailed information for vg1111292651:

Variant ID: vg1111292651 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11292651
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGAGCAGGAAATCAACCATCGGCTGAAGAAGACAAAGCCGAAGCAGGAGTGGCGTGTTAAGAATCAAGTTCCTGTAGTTGAGGAAGCCACAGCCGATGA[A/G]
GCAAAAAGGTTGGCCAAAGGAAAAAGTGTTGTAACTGCTCCGATCAACATGGTTTTCACGTTGCCTGCCGAGTTTGGGAATAAGCAAGCCGATATTGACG

Reverse complement sequence

CGTCAATATCGGCTTGCTTATTCCCAAACTCGGCAGGCAACGTGAAAACCATGTTGATCGGAGCAGTTACAACACTTTTTCCTTTGGCCAACCTTTTTGC[T/C]
TCATCGGCTGTGGCTTCCTCAACTACAGGAACTTGATTCTTAACACGCCACTCCTGCTTCGGCTTTGTCTTCTTCAGCCGATGGTTGATTTCCTGCTCGA

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	78.30%	0.10%	12.80%	8.72%	NA
All Indica	2759	68.50%	0.30%	19.54%	11.67%	NA
All Japonica	1512	97.50%	0.00%	1.19%	1.32%	NA
Aus	269	64.30%	0.00%	14.87%	20.82%	NA
Indica I	595	59.00%	0.20%	23.03%	17.82%	NA
Indica II	465	67.70%	0.40%	15.27%	16.56%	NA
Indica III	913	74.20%	0.20%	21.69%	3.94%	NA
Indica Intermediate	786	69.70%	0.30%	16.92%	13.10%	NA
Temperate Japonica	767	99.30%	0.00%	0.39%	0.26%	NA
Tropical Japonica	504	94.60%	0.00%	1.98%	3.37%	NA
Japonica Intermediate	241	97.50%	0.00%	2.07%	0.41%	NA
VI/Aromatic	96	96.90%	0.00%	2.08%	1.04%	NA
Intermediate	90	78.90%	0.00%	6.67%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111292651	A -> DEL	LOC_Os11g19590.1	N	frameshift_variant	Average:9.019; most accessible tissue: Callus, score: 22.968	N	N	N	N
vg1111292651	A -> G	LOC_Os11g19590.1	synonymous_variant ; p.Glu249Glu; LOW	synonymous_codon	Average:9.019; most accessible tissue: Callus, score: 22.968	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111292651	7.77E-07	NA	mr1221	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