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Detailed information for vg0217111661:

Variant ID: vg0217111661 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17111661
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.16, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

CATGAGACACGTCACGGCAAAGCTTTTCGATAACCTCGCATTGGCAGTACCCGCTCCATGAAGTTAAATCCTCATGCACTCTAGGCGTCCATGTTTCTAG[T/C]
AGTGAGAGGAGTTCTGGCGCTCCCGGGAAAGAGAAGTCTTACACACATATTAAATTATGGTTCAAGTTAAGTTCTCTCTCTCACACACTCATGGCAGTCC

Reverse complement sequence

GGACTGCCATGAGTGTGTGAGAGAGAGAACTTAACTTGAACCATAATTTAATATGTGTGTAAGACTTCTCTTTCCCGGGAGCGCCAGAACTCCTCTCACT[A/G]
CTAGAAACATGGACGCCTAGAGTGCATGAGGATTTAACTTCATGGAGCGGGTACTGCCAATGCGAGGTTATCGAAAAGCTTTGCCGTGACGTGTCTCATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.50%	28.20%	12.17%	2.14%	NA
All Indica	2759	78.10%	4.70%	14.39%	2.83%	NA
All Japonica	1512	22.30%	77.20%	0.46%	0.07%	NA
Aus	269	33.50%	0.40%	58.74%	7.43%	NA
Indica I	595	77.10%	0.70%	16.13%	6.05%	NA
Indica II	465	63.40%	10.10%	20.43%	6.02%	NA
Indica III	913	83.10%	5.80%	10.95%	0.11%	NA
Indica Intermediate	786	81.70%	3.20%	13.49%	1.65%	NA
Temperate Japonica	767	18.80%	81.00%	0.13%	0.13%	NA
Tropical Japonica	504	26.20%	73.00%	0.79%	0.00%	NA
Japonica Intermediate	241	25.30%	73.90%	0.83%	0.00%	NA
VI/Aromatic	96	87.50%	8.30%	3.12%	1.04%	NA
Intermediate	90	57.80%	30.00%	11.11%	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
vg0217111661	T -> DEL	N	N	silent_mutation	Average:52.016; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0217111661	T -> C	LOC_Os02g28890.1	upstream_gene_variant ; 1199.0bp to feature; MODIFIER	silent_mutation	Average:52.016; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N
vg0217111661	T -> C	LOC_Os02g28890-LOC_Os02g28900	intergenic_region ; MODIFIER	silent_mutation	Average:52.016; most accessible tissue: Minghui63 panicle, score: 76.913	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217111661	NA	3.86E-41	mr1093	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
vg0217111661	NA	2.03E-06	mr1408	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
vg0217111661	NA	6.00E-29	mr1423	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
vg0217111661	NA	8.02E-29	mr1546	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
vg0217111661	NA	6.24E-06	mr1897	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
vg0217111661	1.27E-06	NA	mr1064_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
vg0217111661	NA	1.46E-07	mr1399_2	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
vg0217111661	NA	1.20E-07	mr1683_2	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
vg0217111661	NA	2.59E-06	mr1687_2	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
vg0217111661	NA	2.52E-13	mr1838_2	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
vg0217111661	9.51E-07	1.82E-10	mr1897_2	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
vg0217111661	5.04E-07	5.04E-07	mr1897_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
vg0217111661	2.55E-06	NA	mr1914_2	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
vg0217111661	8.97E-06	8.97E-06	mr1914_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