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Detailed information for vg1214358313:

Variant ID: vg1214358313 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14358313
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTTTAATAACATGTGCAAGGGTATGTTAATTTTTTTTTATAAAATGTGGAGGATATGTTTGCCTTTTTAATTTTTTTTAAACAACATGTCGAGGAAAT[G/A]
TAATTGGGAATTAGTGCACTACTTAATAATAACAAATCAAATTTTGTACAAATATGTTTGTACTAATTAATTTAGCAAATTAGTTTGTACTAATTAATAA

Reverse complement sequence

TTATTAATTAGTACAAACTAATTTGCTAAATTAATTAGTACAAACATATTTGTACAAAATTTGATTTGTTATTATTAAGTAGTGCACTAATTCCCAATTA[C/T]
ATTTCCTCGACATGTTGTTTAAAAAAAATTAAAAAGGCAAACATATCCTCCACATTTTATAAAAAAAAATTAACATACCCTTGCACATGTTATTAAACAA

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	65.10%	0.40%	3.05%	31.53%	NA
All Indica	2759	48.70%	0.60%	3.01%	47.70%	NA
All Japonica	1512	99.40%	0.00%	0.00%	0.60%	NA
Aus	269	45.00%	0.00%	15.24%	39.78%	NA
Indica I	595	38.30%	0.50%	1.51%	59.66%	NA
Indica II	465	65.40%	0.00%	1.94%	32.69%	NA
Indica III	913	46.40%	1.10%	3.72%	48.74%	NA
Indica Intermediate	786	49.20%	0.50%	3.94%	46.31%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	39.60%	0.00%	18.75%	41.67%	NA
Intermediate	90	77.80%	0.00%	2.22%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214358313	G -> DEL	N	N	silent_mutation	Average:18.04; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N
vg1214358313	G -> A	LOC_Os12g25020.1	upstream_gene_variant ; 417.0bp to feature; MODIFIER	silent_mutation	Average:18.04; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N
vg1214358313	G -> A	LOC_Os12g25030.1	upstream_gene_variant ; 2263.0bp to feature; MODIFIER	silent_mutation	Average:18.04; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N
vg1214358313	G -> A	LOC_Os12g25000.1	downstream_gene_variant ; 2151.0bp to feature; MODIFIER	silent_mutation	Average:18.04; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N
vg1214358313	G -> A	LOC_Os12g25010.1	downstream_gene_variant ; 1542.0bp to feature; MODIFIER	silent_mutation	Average:18.04; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N
vg1214358313	G -> A	LOC_Os12g25010-LOC_Os12g25020	intergenic_region ; MODIFIER	silent_mutation	Average:18.04; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214358313	1.71E-06	NA	mr1004	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
vg1214358313	1.24E-06	NA	mr1005	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