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Detailed information for vg1220111154:

Variant ID: vg1220111154 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20111154
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATTGGCGCCGGCTGTGTACGACGCGTGGGCTCGACGTGGCAGCGCCGAACCGAGGCTTCACCTCCACCCAGCTGCGTCGCCACTCTTCACCCACCATCC[C/T]
AGTGCCGATCCAACCGAGGGAGGAAGCTCCAGCTCTCCCTCTCCACCTCTCTTTTGTCGCCGGCCGCCAAGAAGAGGGACATCGCCAACCATCGTCGAGC

Reverse complement sequence

GCTCGACGATGGTTGGCGATGTCCCTCTTCTTGGCGGCCGGCGACAAAAGAGAGGTGGAGAGGGAGAGCTGGAGCTTCCTCCCTCGGTTGGATCGGCACT[G/A]
GGATGGTGGGTGAAGAGTGGCGACGCAGCTGGGTGGAGGTGAAGCCTCGGTTCGGCGCTGCCACGTCGAGCCCACGCGTCGTACACAGCCGGCGCCAATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.70%	11.90%	11.30%	8.15%	NA
All Indica	2759	65.70%	18.40%	14.64%	1.23%	NA
All Japonica	1512	75.30%	0.10%	4.56%	19.97%	NA
Aus	269	75.10%	12.30%	12.27%	0.37%	NA
Indica I	595	59.70%	7.20%	28.57%	4.54%	NA
Indica II	465	83.00%	7.30%	9.46%	0.22%	NA
Indica III	913	59.90%	34.10%	5.91%	0.11%	NA
Indica Intermediate	786	66.70%	15.40%	17.30%	0.64%	NA
Temperate Japonica	767	94.70%	0.00%	0.65%	4.69%	NA
Tropical Japonica	504	48.40%	0.40%	4.96%	46.23%	NA
Japonica Intermediate	241	70.10%	0.00%	16.18%	13.69%	NA
VI/Aromatic	96	26.00%	10.40%	20.83%	42.71%	NA
Intermediate	90	75.60%	7.80%	8.89%	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
vg1220111154	C -> DEL	N	N	silent_mutation	Average:24.391; most accessible tissue: Callus, score: 56.531	N	N	N	N
vg1220111154	C -> T	LOC_Os12g33240.1	downstream_gene_variant ; 3134.0bp to feature; MODIFIER	silent_mutation	Average:24.391; most accessible tissue: Callus, score: 56.531	N	N	N	N
vg1220111154	C -> T	LOC_Os12g33240.2	downstream_gene_variant ; 3134.0bp to feature; MODIFIER	silent_mutation	Average:24.391; most accessible tissue: Callus, score: 56.531	N	N	N	N
vg1220111154	C -> T	LOC_Os12g33240.3	downstream_gene_variant ; 3134.0bp to feature; MODIFIER	silent_mutation	Average:24.391; most accessible tissue: Callus, score: 56.531	N	N	N	N
vg1220111154	C -> T	LOC_Os12g33240-LOC_Os12g33250	intergenic_region ; MODIFIER	silent_mutation	Average:24.391; most accessible tissue: Callus, score: 56.531	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220111154	2.40E-07	5.82E-07	mr1993	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
vg1220111154	8.46E-07	8.46E-07	mr1993	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