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Detailed information for vg1219437108:

Variant ID: vg1219437108 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19437108
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

CGCCTCAAACGGATCAGCCGCCGCCACACCGCCTCCTCCCACGAAGCAAGTCGCCGCCGACAAAGCAACTCGCCGCCAACAAAGCACGAAGCAACTCGCC[G/T]
CCGCCTCCCACGGATCGGATCAGAAAGGAATGGCTGAGATTTGGTAGAAAACCCTATTTCCCTCCCCGGACACTCACACTCCTACGCGAAAAGACAAATT

Reverse complement sequence

AATTTGTCTTTTCGCGTAGGAGTGTGAGTGTCCGGGGAGGGAAATAGGGTTTTCTACCAAATCTCAGCCATTCCTTTCTGATCCGATCCGTGGGAGGCGG[C/A]
GGCGAGTTGCTTCGTGCTTTGTTGGCGGCGAGTTGCTTTGTCGGCGGCGACTTGCTTCGTGGGAGGAGGCGGTGTGGCGGCGGCTGATCCGTTTGAGGCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.10%	6.80%	0.11%	0.00%	NA
All Indica	2759	90.30%	9.60%	0.14%	0.00%	NA
All Japonica	1512	99.00%	0.90%	0.07%	0.00%	NA
Aus	269	85.50%	14.50%	0.00%	0.00%	NA
Indica I	595	80.20%	19.50%	0.34%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	91.50%	8.40%	0.11%	0.00%	NA
Indica Intermediate	786	92.50%	7.40%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	96.30%	3.30%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg1219437108	G -> T	LOC_Os12g32210.1	upstream_gene_variant ; 4068.0bp to feature; MODIFIER	silent_mutation	Average:53.15; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg1219437108	G -> T	LOC_Os12g32210.2	upstream_gene_variant ; 3610.0bp to feature; MODIFIER	silent_mutation	Average:53.15; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg1219437108	G -> T	LOC_Os12g32200.1	intron_variant ; MODIFIER	silent_mutation	Average:53.15; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219437108	5.70E-06	1.11E-06	mr1111	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
vg1219437108	3.54E-06	NA	mr1588	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
vg1219437108	NA	1.72E-06	mr1588	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