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Detailed information for vg1211683413:

Variant ID: vg1211683413 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 11683413
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCAACAGCGCAGCCTTCCTGTCTTTTCCAGGCTAGCGCTTACACATGTTTTATAATTGCAAAACCTAATCACAATAATCCGTAAATCTCCATGTAACA[A/G]
CATTAAACTTCGGATGATCATATCTTGGTCATACGAACCCTGAATCGACCCATTCAAGTCTCCTAATGTTTGTTATAACATAAAGAACCGTGTGCTTTCT

Reverse complement sequence

AGAAAGCACACGGTTCTTTATGTTATAACAAACATTAGGAGACTTGAATGGGTCGATTCAGGGTTCGTATGACCAAGATATGATCATCCGAAGTTTAATG[T/C]
TGTTACATGGAGATTTACGGATTATTGTGATTAGGTTTTGCAATTATAAAACATGTGTAAGCGCTAGCCTGGAAAAGACAGGAAGGCTGCGCTGTTGACA

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	83.10%	0.60%	4.87%	11.45%	NA
All Indica	2759	88.30%	0.80%	5.33%	5.65%	NA
All Japonica	1512	76.70%	0.20%	1.85%	21.30%	NA
Aus	269	63.20%	0.70%	16.73%	19.33%	NA
Indica I	595	98.00%	0.20%	0.84%	1.01%	NA
Indica II	465	78.90%	1.10%	10.11%	9.89%	NA
Indica III	913	86.70%	1.20%	5.04%	7.01%	NA
Indica Intermediate	786	88.20%	0.50%	6.23%	5.09%	NA
Temperate Japonica	767	94.80%	0.10%	0.39%	4.69%	NA
Tropical Japonica	504	49.60%	0.40%	4.17%	45.83%	NA
Japonica Intermediate	241	75.50%	0.00%	1.66%	22.82%	NA
VI/Aromatic	96	89.60%	0.00%	6.25%	4.17%	NA
Intermediate	90	87.80%	0.00%	4.44%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1211683413	A -> DEL	N	N	silent_mutation	Average:33.052; most accessible tissue: Zhenshan97 flag leaf, score: 74.825	N	N	N	N
vg1211683413	A -> G	LOC_Os12g20090.1	upstream_gene_variant ; 3871.0bp to feature; MODIFIER	silent_mutation	Average:33.052; most accessible tissue: Zhenshan97 flag leaf, score: 74.825	N	N	N	N
vg1211683413	A -> G	LOC_Os12g20100.1	downstream_gene_variant ; 3195.0bp to feature; MODIFIER	silent_mutation	Average:33.052; most accessible tissue: Zhenshan97 flag leaf, score: 74.825	N	N	N	N
vg1211683413	A -> G	LOC_Os12g20090-LOC_Os12g20100	intergenic_region ; MODIFIER	silent_mutation	Average:33.052; most accessible tissue: Zhenshan97 flag leaf, score: 74.825	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1211683413	3.60E-06	NA	mr1109	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