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Detailed information for vg0219499870:

Variant ID: vg0219499870 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 19499870
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGTTTTCTCTTCACTTGCCACCCCCATTGAGCTTGCTGTCTCAATAGGGAGACATGGCATCCCGACGACCTCTTTCATCCACGTCATCCCTCCCAACT[C/T]
AGGATCGCTGCCAACCTCTGATCTAATAATGTCATCATCCTCTTATGCGGCAATGTGGATCTTAGATCCGGTGCCGCTGAACTTTGATTTTATAGATCAT

Reverse complement sequence

ATGATCTATAAAATCAAAGTTCAGCGGCACCGGATCTAAGATCCACATTGCCGCATAAGAGGATGATGACATTATTAGATCAGAGGTTGGCAGCGATCCT[G/A]
AGTTGGGAGGGATGACGTGGATGAAAGAGGTCGTCGGGATGCCATGTCTCCCTATTGAGACAGCAAGCTCAATGGGGGTGGCAAGTGAAGAGAAAACGGC

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	88.20%	11.30%	0.55%	0.00%	NA
All Indica	2759	88.80%	10.70%	0.54%	0.00%	NA
All Japonica	1512	98.50%	1.30%	0.20%	0.00%	NA
Aus	269	40.50%	57.20%	2.23%	0.00%	NA
Indica I	595	75.10%	23.00%	1.85%	0.00%	NA
Indica II	465	94.40%	5.60%	0.00%	0.00%	NA
Indica III	913	97.50%	2.50%	0.00%	0.00%	NA
Indica Intermediate	786	85.60%	13.90%	0.51%	0.00%	NA
Temperate Japonica	767	99.50%	0.30%	0.26%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	5.00%	0.41%	0.00%	NA
VI/Aromatic	96	42.70%	56.20%	1.04%	0.00%	NA
Intermediate	90	88.90%	10.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0219499870	C -> T	LOC_Os02g32850.1	upstream_gene_variant ; 3630.0bp to feature; MODIFIER	silent_mutation	Average:59.922; most accessible tissue: Zhenshan97 panicle, score: 89.846	N	N	N	N
vg0219499870	C -> T	LOC_Os02g32840-LOC_Os02g32850	intergenic_region ; MODIFIER	silent_mutation	Average:59.922; most accessible tissue: Zhenshan97 panicle, score: 89.846	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0219499870	NA	1.07E-07	mr1662	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
vg0219499870	NA	7.45E-06	mr1265_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
vg0219499870	NA	1.58E-08	mr1627_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
vg0219499870	NA	4.01E-06	mr1895_2	Ind_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