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Detailed information for vg0220195397:

Variant ID: vg0220195397 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20195397
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, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:

TTACAAGCCCTTCTCCACATCCAACTCGGGATAGAAACCAATAGAAACACGAAACATGCCTTCCCAAGCAAGGAAACCCGAGACCCGACGAAAACAGACT[C/T]
GGACTCGGACCCTGACAGTCTGACCGCCCACATACCTGCGGTCAGACCGGCCCTACTAGCCGGTCAGACCGCCCATATACCTGCGGTCTGACCGGCCCTG

Reverse complement sequence

CAGGGCCGGTCAGACCGCAGGTATATGGGCGGTCTGACCGGCTAGTAGGGCCGGTCTGACCGCAGGTATGTGGGCGGTCAGACTGTCAGGGTCCGAGTCC[G/A]
AGTCTGTTTTCGTCGGGTCTCGGGTTTCCTTGCTTGGGAAGGCATGTTTCGTGTTTCTATTGGTTTCTATCCCGAGTTGGATGTGGAGAAGGGCTTGTAA

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	92.40%	6.50%	0.78%	0.34%	NA
All Indica	2759	87.70%	10.40%	1.23%	0.58%	NA
All Japonica	1512	99.10%	0.80%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.30%	1.70%	1.01%	0.00%	NA
Indica II	465	69.90%	27.50%	1.29%	1.29%	NA
Indica III	913	90.90%	7.80%	0.44%	0.88%	NA
Indica Intermediate	786	87.40%	10.10%	2.29%	0.25%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	8.90%	2.22%	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
vg0220195397	C -> T	LOC_Os02g33890.1	downstream_gene_variant ; 279.0bp to feature; MODIFIER	silent_mutation	Average:53.98; most accessible tissue: Zhenshan97 root, score: 66.289	N	N	N	N
vg0220195397	C -> T	LOC_Os02g33860-LOC_Os02g33890	intergenic_region ; MODIFIER	silent_mutation	Average:53.98; most accessible tissue: Zhenshan97 root, score: 66.289	N	N	N	N
vg0220195397	C -> DEL	N	N	silent_mutation	Average:53.98; most accessible tissue: Zhenshan97 root, score: 66.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220195397	2.50E-06	NA	mr1412	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
vg0220195397	1.46E-06	1.46E-06	mr1412	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