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Detailed information for vg1216757160:

Variant ID: vg1216757160 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16757160
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCGGACCATTGTTATTGAAGAACATGGCTTGGACGAGTGGTGTAGCGGCGTTGGCGACTTTCATCTCTACCTCCCTCAAGCCTCTTAATTTTGTTGACC[A/G]
AGACATCGAATTGAGCCTGAGATTTGATCTTGCGATCTACATAAATAGATTTATATCAACGAGTGGGCATAAAGAAAAGAATGGTTTTTAAAGTATTAGT

Reverse complement sequence

ACTAATACTTTAAAAACCATTCTTTTCTTTATGCCCACTCGTTGATATAAATCTATTTATGTAGATCGCAAGATCAAATCTCAGGCTCAATTCGATGTCT[T/C]
GGTCAACAAAATTAAGAGGCTTGAGGGAGGTAGAGATGAAAGTCGCCAACGCCGCTACACCACTCGTCCAAGCCATGTTCTTCAATAACAATGGTCCGAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.90%	15.70%	5.73%	22.64%	NA
All Indica	2759	35.30%	19.00%	8.48%	37.22%	NA
All Japonica	1512	94.20%	3.20%	1.52%	1.06%	NA
Aus	269	33.80%	56.50%	2.60%	7.06%	NA
Indica I	595	48.90%	27.10%	5.88%	18.15%	NA
Indica II	465	50.80%	5.60%	8.17%	35.48%	NA
Indica III	913	14.50%	19.90%	10.08%	55.53%	NA
Indica Intermediate	786	39.90%	19.80%	8.78%	31.42%	NA
Temperate Japonica	767	97.30%	1.70%	0.65%	0.39%	NA
Tropical Japonica	504	90.30%	5.00%	2.78%	1.98%	NA
Japonica Intermediate	241	92.50%	4.60%	1.66%	1.24%	NA
VI/Aromatic	96	90.60%	7.30%	1.04%	1.04%	NA
Intermediate	90	73.30%	12.20%	6.67%	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
vg1216757160	A -> DEL	N	N	silent_mutation	Average:6.308; most accessible tissue: Zhenshan97 young leaf, score: 16.166	N	N	N	N
vg1216757160	A -> G	LOC_Os12g28330.1	downstream_gene_variant ; 765.0bp to feature; MODIFIER	silent_mutation	Average:6.308; most accessible tissue: Zhenshan97 young leaf, score: 16.166	N	N	N	N
vg1216757160	A -> G	LOC_Os12g28340.1	intron_variant ; MODIFIER	silent_mutation	Average:6.308; most accessible tissue: Zhenshan97 young leaf, score: 16.166	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216757160	NA	7.61E-06	mr1864	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1216757160	3.09E-06	3.08E-06	mr1207_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