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Detailed information for vg1216561117:

Variant ID: vg1216561117 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16561117
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCAAGTCATGTTATGTATATTTAATTGTGCAAGTCACAAATTAAGAGATACAAAATTCTAGCGTCCACATAATGGAGCTATGAGTCATAAATGAGGTA[G/C]
AATAATCTTCTCTTATTAGAGCTTTTGATGAGCTCCCACTGATTGTATTATTTATTTAATGGAAGCATAATATCTTATTTTTCATAAACTTGAATCACTT

Reverse complement sequence

AAGTGATTCAAGTTTATGAAAAATAAGATATTATGCTTCCATTAAATAAATAATACAATCAGTGGGAGCTCATCAAAAGCTCTAATAAGAGAAGATTATT[C/G]
TACCTCATTTATGACTCATAGCTCCATTATGTGGACGCTAGAATTTTGTATCTCTTAATTTGTGACTTGCACAATTAAATATACATAACATGACTTGAGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.10%	6.90%	2.26%	2.75%	NA
All Indica	2759	96.90%	0.10%	1.38%	1.56%	NA
All Japonica	1512	78.50%	20.60%	0.93%	0.00%	NA
Aus	269	46.10%	2.60%	19.70%	31.60%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	99.40%	0.20%	0.43%	0.00%	NA
Indica III	913	96.90%	0.00%	1.75%	1.31%	NA
Indica Intermediate	786	93.30%	0.40%	2.54%	3.82%	NA
Temperate Japonica	767	84.90%	14.10%	1.04%	0.00%	NA
Tropical Japonica	504	75.00%	24.20%	0.79%	0.00%	NA
Japonica Intermediate	241	65.60%	33.60%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	91.10%	5.60%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216561117	G -> C	LOC_Os12g28065.1	downstream_gene_variant ; 3910.0bp to feature; MODIFIER	silent_mutation	Average:17.806; most accessible tissue: Zhenshan97 root, score: 25.639	N	N	N	N
vg1216561117	G -> C	LOC_Os12g28050-LOC_Os12g28065	intergenic_region ; MODIFIER	silent_mutation	Average:17.806; most accessible tissue: Zhenshan97 root, score: 25.639	N	N	N	N
vg1216561117	G -> DEL	N	N	silent_mutation	Average:17.806; most accessible tissue: Zhenshan97 root, score: 25.639	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216561117	4.74E-07	2.79E-07	mr1071_2	Jap_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
vg1216561117	5.96E-07	4.88E-07	mr1080_2	Jap_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
vg1216561117	NA	9.01E-08	mr1137_2	Jap_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
vg1216561117	8.02E-07	8.61E-07	mr1203_2	Jap_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
vg1216561117	4.26E-08	2.50E-06	mr1613_2	Jap_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
vg1216561117	NA	4.70E-06	mr1617_2	Jap_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
vg1216561117	5.13E-06	9.20E-07	mr1619_2	Jap_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
vg1216561117	7.24E-06	NA	mr1795_2	Jap_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