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Detailed information for vg1108252692:

Variant ID: vg1108252692 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8252692
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGGTTACCCATAGAAGCTCTCTAAAAATATTGGAAAAGTAGAACTATTCTCCTCTCTTTCTCTTTTAATTAAACCAAACTAATGGCACATGCAGTTATA[G/A]
TCTCTTTAATTGTTCTCATTCAAAATTTATTTATTATTTCCTGTGTTATTAGTACCGTACATCTATTACTGTACTAATGGCCCATTTACCAGCAAAAGTT

Reverse complement sequence

AACTTTTGCTGGTAAATGGGCCATTAGTACAGTAATAGATGTACGGTACTAATAACACAGGAAATAATAAATAAATTTTGAATGAGAACAATTAAAGAGA[C/T]
TATAACTGCATGTGCCATTAGTTTGGTTTAATTAAAAGAGAAAGAGAGGAGAATAGTTCTACTTTTCCAATATTTTTAGAGAGCTTCTATGGGTAACCAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.60%	0.20%	0.57%	58.68%	NA
All Indica	2759	6.70%	0.30%	0.83%	92.13%	NA
All Japonica	1512	93.10%	0.00%	0.13%	6.81%	NA
Aus	269	72.90%	0.00%	0.37%	26.77%	NA
Indica I	595	9.20%	0.30%	1.34%	89.08%	NA
Indica II	465	2.60%	0.00%	0.86%	96.56%	NA
Indica III	913	3.00%	0.40%	0.77%	95.84%	NA
Indica Intermediate	786	11.70%	0.30%	0.51%	87.53%	NA
Temperate Japonica	767	97.90%	0.00%	0.00%	2.09%	NA
Tropical Japonica	504	89.10%	0.00%	0.40%	10.52%	NA
Japonica Intermediate	241	85.90%	0.00%	0.00%	14.11%	NA
VI/Aromatic	96	89.60%	0.00%	0.00%	10.42%	NA
Intermediate	90	47.80%	0.00%	1.11%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108252692	G -> A	LOC_Os11g14630.1	upstream_gene_variant ; 4350.0bp to feature; MODIFIER	silent_mutation	Average:8.494; most accessible tissue: Callus, score: 36.754	N	N	N	N
vg1108252692	G -> A	LOC_Os11g14650.1	upstream_gene_variant ; 1437.0bp to feature; MODIFIER	silent_mutation	Average:8.494; most accessible tissue: Callus, score: 36.754	N	N	N	N
vg1108252692	G -> A	LOC_Os11g14640.1	intron_variant ; MODIFIER	silent_mutation	Average:8.494; most accessible tissue: Callus, score: 36.754	N	N	N	N
vg1108252692	G -> DEL	N	N	silent_mutation	Average:8.494; most accessible tissue: Callus, score: 36.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108252692	5.62E-06	5.63E-06	mr1480	Jap_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
vg1108252692	NA	9.66E-07	mr1692	Jap_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
vg1108252692	NA	5.80E-10	mr1228_2	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