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Detailed information for vg0203137192:

Variant ID: vg0203137192 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3137192
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.33, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

TTGAGCAGTTTTGAAAGCCAACGAGGTATTTTTTCCAGACAACGAGCAAGAAGGTACCGAAAGAACCTGAAGACTCTGAAAACCATCAACTATTGGTATG[C/T]
CATCTGGCATGGCCTTGCCCTTGAAGTTGATTCCCATAATCAAAGTGTTGACTTTTTGCAGTTCTTGAGTGCATGAATTGCATTTGAGATATTCCCAAAA

Reverse complement sequence

TTTTGGGAATATCTCAAATGCAATTCATGCACTCAAGAACTGCAAAAAGTCAACACTTTGATTATGGGAATCAACTTCAAGGGCAAGGCCATGCCAGATG[G/A]
CATACCAATAGTTGATGGTTTTCAGAGTCTTCAGGTTCTTTCGGTACCTTCTTGCTCGTTGTCTGGAAAAAATACCTCGTTGGCTTTCAAAACTGCTCAA

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	54.90%	42.70%	0.02%	2.33%	NA
All Indica	2759	38.30%	59.10%	0.04%	2.54%	NA
All Japonica	1512	90.60%	9.20%	0.00%	0.20%	NA
Aus	269	17.10%	82.50%	0.00%	0.37%	NA
Indica I	595	53.30%	46.70%	0.00%	0.00%	NA
Indica II	465	53.50%	46.20%	0.00%	0.22%	NA
Indica III	913	17.90%	77.90%	0.00%	4.27%	NA
Indica Intermediate	786	41.90%	54.20%	0.13%	3.82%	NA
Temperate Japonica	767	84.40%	15.60%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	93.80%	5.00%	0.00%	1.24%	NA
VI/Aromatic	96	64.60%	4.20%	0.00%	31.25%	NA
Intermediate	90	66.70%	26.70%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203137192	C -> T	LOC_Os02g06270.1	upstream_gene_variant ; 2207.0bp to feature; MODIFIER	silent_mutation	Average:49.409; most accessible tissue: Callus, score: 84.278	N	N	N	N
vg0203137192	C -> T	LOC_Os02g06290.1	upstream_gene_variant ; 4800.0bp to feature; MODIFIER	silent_mutation	Average:49.409; most accessible tissue: Callus, score: 84.278	N	N	N	N
vg0203137192	C -> T	LOC_Os02g06280.1	intron_variant ; MODIFIER	silent_mutation	Average:49.409; most accessible tissue: Callus, score: 84.278	N	N	N	N
vg0203137192	C -> DEL	N	N	silent_mutation	Average:49.409; most accessible tissue: Callus, score: 84.278	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203137192	NA	1.85E-06	mr1517_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
vg0203137192	NA	6.83E-09	mr1582_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
vg0203137192	NA	1.53E-06	mr1582_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