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Detailed information for vg0206284604:

Variant ID: vg0206284604 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6284604
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.56, C: 0.44, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

CTATTTATCCAAAAAATACGTTACGTCTCCCTATTTATGAAAATTGCCGTTTACATTTGGTTGCATCTTATAGTCTTTTGCTTCAGTTTGCGCCTTGGGA[T/C]
TGGATAGGACAGCATCTGGCAGACTAGCACATAGACCTATTTAGCTCTTCCATTAAAATTTCTTGATAAACACCATTGCTAAATTTTATTTTATTTTAAG

Reverse complement sequence

CTTAAAATAAAATAAAATTTAGCAATGGTGTTTATCAAGAAATTTTAATGGAAGAGCTAAATAGGTCTATGTGCTAGTCTGCCAGATGCTGTCCTATCCA[A/G]
TCCCAAGGCGCAAACTGAAGCAAAAGACTATAAGATGCAACCAAATGTAAACGGCAATTTTCATAAATAGGGAGACGTAACGTATTTTTTGGATAAATAG

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	81.70%	10.30%	0.76%	7.28%	NA
All Indica	2759	79.30%	16.20%	0.22%	4.28%	NA
All Japonica	1512	97.60%	1.70%	0.26%	0.53%	NA
Aus	269	30.50%	0.00%	7.81%	61.71%	NA
Indica I	595	93.30%	6.70%	0.00%	0.00%	NA
Indica II	465	65.20%	26.50%	0.22%	8.17%	NA
Indica III	913	76.60%	19.60%	0.33%	3.50%	NA
Indica Intermediate	786	80.20%	13.50%	0.25%	6.11%	NA
Temperate Japonica	767	98.60%	0.90%	0.52%	0.00%	NA
Tropical Japonica	504	96.20%	3.00%	0.00%	0.79%	NA
Japonica Intermediate	241	97.10%	1.20%	0.00%	1.66%	NA
VI/Aromatic	96	44.80%	8.30%	3.12%	43.75%	NA
Intermediate	90	80.00%	6.70%	2.22%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0206284604	T -> DEL	N	N	silent_mutation	Average:27.365; most accessible tissue: Minghui63 flower, score: 34.612	N	N	N	N
vg0206284604	T -> C	LOC_Os02g12100-LOC_Os02g12110	intergenic_region ; MODIFIER	silent_mutation	Average:27.365; most accessible tissue: Minghui63 flower, score: 34.612	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206284604	NA	4.29E-06	mr1004	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
vg0206284604	NA	2.36E-08	mr1006	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
vg0206284604	NA	4.92E-08	mr1007	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
vg0206284604	NA	8.74E-06	mr1007	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
vg0206284604	NA	5.11E-06	mr1037	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
vg0206284604	NA	5.00E-08	mr1052	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
vg0206284604	NA	2.92E-13	mr1004_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
vg0206284604	NA	2.36E-07	mr1004_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
vg0206284604	NA	1.79E-07	mr1006_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