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Detailed information for vg1200051954:

Variant ID: vg1200051954 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 51954
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGTTAGTCCAACGTGTTGAATAGTGTCGGGTGAGAAGAATATATAAATATTAGACACGTTATATTAAACCTCAGGGTAGAGGAGGTATATAAGGAAAC[G/A]
AGTCTATTCAAATCAATTCTATCATAAGATATATTTTACTACCATATACTCTAACATCCCCCACAATACAAGCGTGAGCAACACAGACGCTTATATTAGA

Reverse complement sequence

TCTAATATAAGCGTCTGTGTTGCTCACGCTTGTATTGTGGGGGATGTTAGAGTATATGGTAGTAAAATATATCTTATGATAGAATTGATTTGAATAGACT[C/T]
GTTTCCTTATATACCTCCTCTACCCTGAGGTTTAATATAACGTGTCTAATATTTATATATTCTTCTCACCCGACACTATTCAACACGTTGGACTAACAAA

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	78.30%	6.20%	3.17%	12.36%	NA
All Indica	2759	67.10%	8.60%	4.82%	19.50%	NA
All Japonica	1512	93.50%	3.00%	0.73%	2.78%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	80.20%	1.80%	1.85%	16.13%	NA
Indica II	465	41.90%	32.70%	9.03%	16.34%	NA
Indica III	913	66.20%	4.40%	5.91%	23.55%	NA
Indica Intermediate	786	73.30%	4.20%	3.31%	19.21%	NA
Temperate Japonica	767	93.50%	4.40%	1.04%	1.04%	NA
Tropical Japonica	504	93.50%	1.80%	0.60%	4.17%	NA
Japonica Intermediate	241	93.80%	0.80%	0.00%	5.39%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	81.10%	8.90%	6.67%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1200051954	G -> DEL	N	N	silent_mutation	Average:16.967; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N
vg1200051954	G -> A	LOC_Os12g01090.1	downstream_gene_variant ; 1852.0bp to feature; MODIFIER	silent_mutation	Average:16.967; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N
vg1200051954	G -> A	LOC_Os12g01100.1	downstream_gene_variant ; 276.0bp to feature; MODIFIER	silent_mutation	Average:16.967; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N
vg1200051954	G -> A	LOC_Os12g01110.1	downstream_gene_variant ; 96.0bp to feature; MODIFIER	silent_mutation	Average:16.967; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N
vg1200051954	G -> A	LOC_Os12g01100-LOC_Os12g01110	intergenic_region ; MODIFIER	silent_mutation	Average:16.967; most accessible tissue: Zhenshan97 flag leaf, score: 27.583	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200051954	9.52E-07	2.10E-08	mr1893_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