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Detailed information for vg1200594974:

Variant ID: vg1200594974 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 594974
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTAGCGATTGCACGGCGTCTTGGACTTGTTCTGGTTGGTAGCCACGTCGCAAACGTCGCACTCGATCAAAGCGAGAGTTATCCCCCTCACCAGAAGATC[G/A]
GGCCACGAGAGAGAGTGTCATCACGCTGGAGGGCAGAGGCAGTCCATTGTGGTGGGGATCTCGTCCGCCGTGGGGGCTCGTAGGGGCATTCGCTGCTGCC

Reverse complement sequence

GGCAGCAGCGAATGCCCCTACGAGCCCCCACGGCGGACGAGATCCCCACCACAATGGACTGCCTCTGCCCTCCAGCGTGATGACACTCTCTCTCGTGGCC[C/T]
GATCTTCTGGTGAGGGGGATAACTCTCGCTTTGATCGAGTGCGACGTTTGCGACGTGGCTACCAACCAGAACAAGTCCAAGACGCCGTGCAATCGCTACA

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	86.00%	5.10%	3.45%	5.46%	NA
All Indica	2759	86.00%	8.60%	4.82%	0.58%	NA
All Japonica	1512	83.70%	0.10%	1.72%	14.48%	NA
Aus	269	98.50%	0.00%	0.00%	1.49%	NA
Indica I	595	89.40%	5.00%	4.87%	0.67%	NA
Indica II	465	97.00%	2.40%	0.43%	0.22%	NA
Indica III	913	80.30%	13.70%	5.48%	0.55%	NA
Indica Intermediate	786	83.50%	9.20%	6.62%	0.76%	NA
Temperate Japonica	767	94.00%	0.10%	0.65%	5.22%	NA
Tropical Japonica	504	71.00%	0.20%	2.98%	25.79%	NA
Japonica Intermediate	241	77.20%	0.00%	2.49%	20.33%	NA
VI/Aromatic	96	80.20%	0.00%	3.12%	16.67%	NA
Intermediate	90	92.20%	3.30%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1200594974	G -> DEL	N	N	silent_mutation	Average:33.062; most accessible tissue: Callus, score: 72.959	N	N	N	N
vg1200594974	G -> A	LOC_Os12g02020.1	upstream_gene_variant ; 4730.0bp to feature; MODIFIER	silent_mutation	Average:33.062; most accessible tissue: Callus, score: 72.959	N	N	N	N
vg1200594974	G -> A	LOC_Os12g02010.1	downstream_gene_variant ; 626.0bp to feature; MODIFIER	silent_mutation	Average:33.062; most accessible tissue: Callus, score: 72.959	N	N	N	N
vg1200594974	G -> A	LOC_Os12g02010-LOC_Os12g02020	intergenic_region ; MODIFIER	silent_mutation	Average:33.062; most accessible tissue: Callus, score: 72.959	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200594974	9.80E-08	9.80E-08	mr1866	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