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Detailed information for vg1219397480:

Variant ID: vg1219397480 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19397480
Reference Allele: G	Alternative Allele: A,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCGAGTTTTCTTGAAGGGATTTCTTATACGACTCCTTTGTTTCCAAGAGTGAATAAAATTAAAACCTGACTCAAATACGGATCTGTATTTCCAAAAAC[G/A,C]
AACGAACTTAAAAACCAACTCATACACGGATGATGTACCAAAGTACCAGCAAAAACATCTTCAATTTTTATCATAGTAGAGATATAAGTCATTGACTACA

Reverse complement sequence

TGTAGTCAATGACTTATATCTCTACTATGATAAAAATTGAAGATGTTTTTGCTGGTACTTTGGTACATCATCCGTGTATGAGTTGGTTTTTAAGTTCGTT[C/T,G]
GTTTTTGGAAATACAGATCCGTATTTGAGTCAGGTTTTAATTTTATTCACTCTTGGAAACAAAGGAGTCGTATAAGAAATCCCTTCAAGAAAACTCGCAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.60%	37.10%	0.23%	0.00%	C: 0.04%
All Indica	2759	39.50%	60.20%	0.33%	0.00%	NA
All Japonica	1512	98.10%	1.70%	0.13%	0.00%	C: 0.13%
Aus	269	84.40%	15.60%	0.00%	0.00%	NA
Indica I	595	39.20%	60.50%	0.34%	0.00%	NA
Indica II	465	61.30%	38.50%	0.22%	0.00%	NA
Indica III	913	24.40%	75.40%	0.22%	0.00%	NA
Indica Intermediate	786	44.40%	55.10%	0.51%	0.00%	NA
Temperate Japonica	767	99.00%	1.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	92.90%	5.40%	0.83%	0.00%	C: 0.83%
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	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
vg1219397480	G -> C	LOC_Os12g32150.1	upstream_gene_variant ; 4750.0bp to feature; MODIFIER	silent_mutation	Average:28.744; most accessible tissue: Callus, score: 57.163	N	N	N	N
vg1219397480	G -> C	LOC_Os12g32150-LOC_Os12g32160	intergenic_region ; MODIFIER	silent_mutation	Average:28.744; most accessible tissue: Callus, score: 57.163	N	N	N	N
vg1219397480	G -> A	LOC_Os12g32150.1	upstream_gene_variant ; 4750.0bp to feature; MODIFIER	silent_mutation	Average:28.744; most accessible tissue: Callus, score: 57.163	N	N	N	N
vg1219397480	G -> A	LOC_Os12g32150-LOC_Os12g32160	intergenic_region ; MODIFIER	silent_mutation	Average:28.744; most accessible tissue: Callus, score: 57.163	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219397480	NA	6.17E-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
vg1219397480	1.28E-06	NA	mr1458_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
vg1219397480	2.31E-06	NA	mr1458_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