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Detailed information for vg1216106203:

Variant ID: vg1216106203 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16106203
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATAGGATAGTAATAATAAGCAGATTCTACTTAAATTTGGAATTTGTTATACGTACAGCAAAATTGTCATCTACATTAGGGTAGACAAAGTATCTCCTAC[A/C]
AATTGTTTGTTCTGCAAACGAGGTAGCCACTTGGCAGCGATCTCTACAACCACACTTTGGACGCTCCGACCATTTAGGTAAACCTAATGGATTGTTCCTC

Reverse complement sequence

GAGGAACAATCCATTAGGTTTACCTAAATGGTCGGAGCGTCCAAAGTGTGGTTGTAGAGATCGCTGCCAAGTGGCTACCTCGTTTGCAGAACAAACAATT[T/G]
GTAGGAGATACTTTGTCTACCCTAATGTAGATGACAATTTTGCTGTACGTATAACAAATTCCAAATTTAAGTAGAATCTGCTTATTATTACTATCCTATC

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	32.20%	25.10%	6.33%	36.35%	NA
All Indica	2759	12.20%	34.30%	9.97%	43.60%	NA
All Japonica	1512	65.50%	6.20%	0.86%	27.45%	NA
Aus	269	24.90%	50.90%	0.74%	23.42%	NA
Indica I	595	25.70%	9.20%	11.26%	53.78%	NA
Indica II	465	10.80%	22.60%	12.26%	54.41%	NA
Indica III	913	3.30%	56.40%	6.46%	33.84%	NA
Indica Intermediate	786	13.10%	34.40%	11.70%	40.84%	NA
Temperate Japonica	767	95.70%	0.00%	0.13%	4.17%	NA
Tropical Japonica	504	14.90%	16.90%	1.59%	66.67%	NA
Japonica Intermediate	241	75.50%	3.30%	1.66%	19.50%	NA
VI/Aromatic	96	82.30%	1.00%	3.12%	13.54%	NA
Intermediate	90	53.30%	13.30%	6.67%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216106203	A -> C	LOC_Os12g27370.1	downstream_gene_variant ; 3379.0bp to feature; MODIFIER	silent_mutation	Average:12.552; most accessible tissue: Callus, score: 30.416	N	N	N	N
vg1216106203	A -> C	LOC_Os12g27390.1	intron_variant ; MODIFIER	silent_mutation	Average:12.552; most accessible tissue: Callus, score: 30.416	N	N	N	N
vg1216106203	A -> DEL	N	N	silent_mutation	Average:12.552; most accessible tissue: Callus, score: 30.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216106203	3.39E-06	4.75E-06	mr1173	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
vg1216106203	NA	8.10E-07	mr1850	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