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Detailed information for vg0114209037:

Variant ID: vg0114209037 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14209037
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.79, C: 0.22, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

CAACCCGACAACGTATGTCGTGTCACATTGTCGGATTCGGCTTAATCGGCTAGCCTTGTCCAACTCGAACTCTGCCGATCCTGGTTGCAGCCGATTCGGA[T/C]
TTTAGCCGATCCTTACTCTGTTTTCGGAACGATTTCCATCTTGAATTCCACTTCAATCTGACCTTCATCTCCGATACTCAGATTACCAAATTTGGTTGTT

Reverse complement sequence

AACAACCAAATTTGGTAATCTGAGTATCGGAGATGAAGGTCAGATTGAAGTGGAATTCAAGATGGAAATCGTTCCGAAAACAGAGTAAGGATCGGCTAAA[A/G]
TCCGAATCGGCTGCAACCAGGATCGGCAGAGTTCGAGTTGGACAAGGCTAGCCGATTAAGCCGAATCCGACAATGTGACACGACATACGTTGTCGGGTTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.50%	31.80%	0.74%	31.95%	NA
All Indica	2759	4.80%	46.60%	1.20%	47.41%	NA
All Japonica	1512	95.40%	4.40%	0.00%	0.13%	NA
Aus	269	2.60%	33.10%	0.74%	63.57%	NA
Indica I	595	3.70%	42.00%	1.51%	52.77%	NA
Indica II	465	4.90%	24.90%	2.37%	67.74%	NA
Indica III	913	5.30%	62.40%	0.22%	32.09%	NA
Indica Intermediate	786	5.00%	44.50%	1.40%	49.11%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	89.50%	10.30%	0.00%	0.20%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	53.10%	44.80%	0.00%	2.08%	NA
Intermediate	90	52.20%	17.80%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114209037	T -> DEL	N	N	silent_mutation	Average:19.036; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0114209037	T -> C	LOC_Os01g25160.1	downstream_gene_variant ; 1442.0bp to feature; MODIFIER	silent_mutation	Average:19.036; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0114209037	T -> C	LOC_Os01g25150-LOC_Os01g25160	intergenic_region ; MODIFIER	silent_mutation	Average:19.036; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114209037	NA	2.15E-06	mr1193	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
vg0114209037	NA	6.05E-09	mr1866	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
vg0114209037	NA	3.13E-07	mr1979	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
vg0114209037	NA	1.38E-07	mr1030_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
vg0114209037	NA	5.58E-06	mr1519_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
vg0114209037	NA	2.63E-07	mr1748_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