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Detailed information for vg1216914223:

Variant ID: vg1216914223 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16914223
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.56, C: 0.45, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

TGCATTGTTCTCTAGCCTGAACATTCCATGTGATATCTTGACCATTTGGACCTCAACTAGCTTCTCCCAAGCCTAGTCTAGATCCATCACTGGCTATACT[A/C]
CCATGGTCTCAAGCAACACCTGCACAAGAACAACAAAGAAACTCTTTATCCGAGTACAAGTTCGTACCAACTTAACTCACATCAACACACAATAGTATCA

Reverse complement sequence

TGATACTATTGTGTGTTGATGTGAGTTAAGTTGGTACGAACTTGTACTCGGATAAAGAGTTTCTTTGTTGTTCTTGTGCAGGTGTTGCTTGAGACCATGG[T/G]
AGTATAGCCAGTGATGGATCTAGACTAGGCTTGGGAGAAGCTAGTTGAGGTCCAAATGGTCAAGATATCACATGGAATGTTCAGGCTAGAGAACAATGCA

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	31.20%	6.50%	0.08%	62.19%	NA
All Indica	2759	11.50%	8.40%	0.11%	79.99%	NA
All Japonica	1512	71.50%	2.90%	0.07%	25.53%	NA
Aus	269	13.40%	5.90%	0.00%	80.67%	NA
Indica I	595	24.20%	8.60%	0.17%	67.06%	NA
Indica II	465	9.70%	4.10%	0.22%	86.02%	NA
Indica III	913	1.80%	12.40%	0.00%	85.87%	NA
Indica Intermediate	786	14.10%	6.40%	0.13%	79.39%	NA
Temperate Japonica	767	93.70%	0.10%	0.00%	6.13%	NA
Tropical Japonica	504	34.50%	8.30%	0.00%	57.14%	NA
Japonica Intermediate	241	78.00%	0.40%	0.41%	21.16%	NA
VI/Aromatic	96	3.10%	11.50%	0.00%	85.42%	NA
Intermediate	90	43.30%	4.40%	0.00%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216914223	A -> C	LOC_Os12g28590.1	downstream_gene_variant ; 3353.0bp to feature; MODIFIER	silent_mutation	Average:15.497; most accessible tissue: Callus, score: 54.602	N	N	N	N
vg1216914223	A -> C	LOC_Os12g28600.1	intron_variant ; MODIFIER	silent_mutation	Average:15.497; most accessible tissue: Callus, score: 54.602	N	N	N	N
vg1216914223	A -> DEL	N	N	silent_mutation	Average:15.497; most accessible tissue: Callus, score: 54.602	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216914223	NA	4.95E-06	mr1060	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
vg1216914223	5.11E-06	NA	mr1686	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
vg1216914223	NA	6.73E-06	mr1686	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
vg1216914223	NA	4.53E-08	mr1458_2	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
vg1216914223	NA	3.23E-06	mr1483_2	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