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Detailed information for vg1206182541:

Variant ID: vg1206182541 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6182541
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: Unkown

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTACATATAACTCTCCCCTAACCATCCACACCATGCTAAGGTTTCACCCCCACCCCCTACCCCGGAGGTGGGCAGTCCCCTCGTGCGCCGCGGTGAATCC[G/A]
GCAGCTGGACAACCGGACACCCCGGCCGACCCAACTCCATCACGCCCACCCTCACCACCGGTGCCTAGGAAAAGGTCGAGCTATACTTCAGATCAAGCAG

Reverse complement sequence

CTGCTTGATCTGAAGTATAGCTCGACCTTTTCCTAGGCACCGGTGGTGAGGGTGGGCGTGATGGAGTTGGGTCGGCCGGGGTGTCCGGTTGTCCAGCTGC[C/T]
GGATTCACCGCGGCGCACGAGGGGACTGCCCACCTCCGGGGTAGGGGGTGGGGGTGAAACCTTAGCATGGTGTGGATGGTTAGGGGAGAGTTATATGTAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of Unkown(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.10%	0.00%	0.38%	12.53%	NA
All Indica	2759	95.40%	0.00%	0.18%	4.42%	NA
All Japonica	1512	71.10%	0.00%	0.60%	28.31%	NA
Aus	269	89.20%	0.00%	1.49%	9.29%	NA
Indica I	595	91.30%	0.00%	0.00%	8.74%	NA
Indica II	465	96.60%	0.00%	0.22%	3.23%	NA
Indica III	913	98.70%	0.00%	0.00%	1.31%	NA
Indica Intermediate	786	94.00%	0.00%	0.51%	5.47%	NA
Temperate Japonica	767	66.40%	0.00%	0.26%	33.38%	NA
Tropical Japonica	504	79.40%	0.00%	1.19%	19.44%	NA
Japonica Intermediate	241	68.90%	0.00%	0.41%	30.71%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	0.00%	0.00%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206182541	G -> A	LOC_Os12g11430.1	upstream_gene_variant ; 2819.0bp to feature; MODIFIER	N	Average:11.883; most accessible tissue: Callus, score: 31.81	N	N	N	N
vg1206182541	G -> A	LOC_Os12g11440.1	upstream_gene_variant ; 1482.0bp to feature; MODIFIER	N	Average:11.883; most accessible tissue: Callus, score: 31.81	N	N	N	N
vg1206182541	G -> A	LOC_Os12g11430-LOC_Os12g11440	intergenic_region ; MODIFIER	N	Average:11.883; most accessible tissue: Callus, score: 31.81	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206182541	8.52E-07	8.52E-07	mr1384	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