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Detailed information for vg1217889336:

Variant ID: vg1217889336 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17889336
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATTATCCTCCCTGGGCGACAAGCGGCGTCTCATGCACCATCTCCTCTGGCTCCGCCATCTCCTCCTCAGGCTCCTGCACCGTCTCCTCCTCATGCTCC[T/A]
GCACCGACTCCTCCTCAGGCTCCTGCACCGACTCCTCCGCAAGCTCCTCGTCCGGCACCTTCCAAGTCAAGGGCCCCCAAGCTTCACCGCCTGCCCCCAC

Reverse complement sequence

GTGGGGGCAGGCGGTGAAGCTTGGGGGCCCTTGACTTGGAAGGTGCCGGACGAGGAGCTTGCGGAGGAGTCGGTGCAGGAGCCTGAGGAGGAGTCGGTGC[A/T]
GGAGCATGAGGAGGAGACGGTGCAGGAGCCTGAGGAGGAGATGGCGGAGCCAGAGGAGATGGTGCATGAGACGCCGCTTGTCGCCCAGGGAGGATAATGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.80%	0.10%	0.49%	8.57%	NA
All Indica	2759	99.60%	0.10%	0.04%	0.29%	NA
All Japonica	1512	76.10%	0.30%	1.26%	22.42%	NA
Aus	269	94.10%	0.00%	0.00%	5.95%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.40%	0.20%	0.00%	0.43%	NA
Indica III	913	99.80%	0.00%	0.00%	0.22%	NA
Indica Intermediate	786	99.40%	0.10%	0.00%	0.51%	NA
Temperate Japonica	767	96.90%	0.00%	0.52%	2.61%	NA
Tropical Japonica	504	52.20%	0.80%	1.98%	45.04%	NA
Japonica Intermediate	241	59.80%	0.00%	2.07%	38.17%	NA
VI/Aromatic	96	58.30%	0.00%	3.12%	38.54%	NA
Intermediate	90	94.40%	0.00%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217889336	T -> DEL	N	N	silent_mutation	Average:33.854; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg1217889336	T -> A	LOC_Os12g29940.1	upstream_gene_variant ; 2738.0bp to feature; MODIFIER	silent_mutation	Average:33.854; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg1217889336	T -> A	LOC_Os12g29920.1	downstream_gene_variant ; 4401.0bp to feature; MODIFIER	silent_mutation	Average:33.854; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg1217889336	T -> A	LOC_Os12g29920-LOC_Os12g29940	intergenic_region ; MODIFIER	silent_mutation	Average:33.854; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217889336	1.11E-06	1.11E-06	mr1184	Jap_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