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Detailed information for vg1206145951:

Variant ID: vg1206145951 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6145951
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.52, A: 0.48, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TAACAATCTATACCTATACTAATTGGGCACTTTCTACAAGCTTCCACGTTAATCAGAAAGATCTAACCGTTAATTAAGTAAATCTTATTATCTTAGCCAT[C/A]
TATTATTAAGCCATGGGCCTTGAAAAGCCCATCGAATCTCCCCCAATACATAAACCTTTTTGTCCATACCTATCAAATCTCTCTCACGTACGTATAGGTA

Reverse complement sequence

TACCTATACGTACGTGAGAGAGATTTGATAGGTATGGACAAAAAGGTTTATGTATTGGGGGAGATTCGATGGGCTTTTCAAGGCCCATGGCTTAATAATA[G/T]
ATGGCTAAGATAATAAGATTTACTTAATTAACGGTTAGATCTTTCTGATTAACGTGGAAGCTTGTAGAAAGTGCCCAATTAGTATAGGTATAGATTGTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.80%	10.70%	0.66%	33.81%	NA
All Indica	2759	82.60%	3.60%	0.47%	13.30%	NA
All Japonica	1512	8.70%	18.50%	1.06%	71.83%	NA
Aus	269	50.60%	8.90%	0.00%	40.52%	NA
Indica I	595	71.30%	2.90%	0.34%	25.55%	NA
Indica II	465	83.90%	3.90%	0.22%	12.04%	NA
Indica III	913	90.80%	2.40%	0.88%	5.91%	NA
Indica Intermediate	786	80.90%	5.50%	0.25%	13.36%	NA
Temperate Japonica	767	12.80%	23.30%	1.56%	62.32%	NA
Tropical Japonica	504	4.80%	4.80%	0.60%	89.88%	NA
Japonica Intermediate	241	3.70%	31.50%	0.41%	64.32%	NA
VI/Aromatic	96	13.50%	84.40%	0.00%	2.08%	NA
Intermediate	90	34.40%	25.60%	2.22%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206145951	C -> DEL	N	N	silent_mutation	Average:8.894; most accessible tissue: Callus, score: 51.15	N	N	N	N
vg1206145951	C -> A	LOC_Os12g11370.1	upstream_gene_variant ; 3793.0bp to feature; MODIFIER	silent_mutation	Average:8.894; most accessible tissue: Callus, score: 51.15	N	N	N	N
vg1206145951	C -> A	LOC_Os12g11380.1	upstream_gene_variant ; 1276.0bp to feature; MODIFIER	silent_mutation	Average:8.894; most accessible tissue: Callus, score: 51.15	N	N	N	N
vg1206145951	C -> A	LOC_Os12g11370-LOC_Os12g11380	intergenic_region ; MODIFIER	silent_mutation	Average:8.894; most accessible tissue: Callus, score: 51.15	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206145951	5.90E-07	2.47E-08	mr1826_2	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