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Detailed information for vg1222100421:

Variant ID: vg1222100421 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22100421
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, G: 0.16, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTGATTGGGATCCTCCAAAGTAAATTCAGAGTGACGTGGTCACTAATATGTAAGCCTCACCACCCATGGGTCAACATGTCATTTGACCATATCAGGTG[A/G]
AAAGTTACGTTAGAGGATTCCTCTCCGAAAAGATTATATCTATTTTGAAAGTGGACCTCTCGGTTATTTACCTTGTGCCAGCTACGAGAAAGCACTACTA

Reverse complement sequence

TAGTAGTGCTTTCTCGTAGCTGGCACAAGGTAAATAACCGAGAGGTCCACTTTCAAAATAGATATAATCTTTTCGGAGAGGAATCCTCTAACGTAACTTT[T/C]
CACCTGATATGGTCAAATGACATGTTGACCCATGGGTGGTGAGGCTTACATATTAGTGACCACGTCACTCTGAATTTACTTTGGAGGATCCCAATCAAGC

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	80.10%	17.90%	0.53%	1.44%	NA
All Indica	2759	92.40%	4.50%	0.80%	2.39%	NA
All Japonica	1512	53.80%	46.00%	0.00%	0.13%	NA
Aus	269	98.50%	0.70%	0.74%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	76.30%	11.60%	2.37%	9.68%	NA
Indica III	913	97.70%	1.60%	0.00%	0.66%	NA
Indica Intermediate	786	91.30%	5.30%	1.40%	1.91%	NA
Temperate Japonica	767	26.10%	73.70%	0.00%	0.26%	NA
Tropical Japonica	504	84.50%	15.50%	0.00%	0.00%	NA
Japonica Intermediate	241	78.00%	22.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	26.70%	1.11%	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
vg1222100421	A -> DEL	N	N	silent_mutation	Average:31.134; most accessible tissue: Callus, score: 91.957	N	N	N	N
vg1222100421	A -> G	LOC_Os12g36060.1	upstream_gene_variant ; 397.0bp to feature; MODIFIER	silent_mutation	Average:31.134; most accessible tissue: Callus, score: 91.957	N	N	N	N
vg1222100421	A -> G	LOC_Os12g36070.1	upstream_gene_variant ; 1528.0bp to feature; MODIFIER	silent_mutation	Average:31.134; most accessible tissue: Callus, score: 91.957	N	N	N	N
vg1222100421	A -> G	LOC_Os12g36050.1	downstream_gene_variant ; 583.0bp to feature; MODIFIER	silent_mutation	Average:31.134; most accessible tissue: Callus, score: 91.957	N	N	N	N
vg1222100421	A -> G	LOC_Os12g36050-LOC_Os12g36060	intergenic_region ; MODIFIER	silent_mutation	Average:31.134; most accessible tissue: Callus, score: 91.957	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222100421	NA	6.39E-07	mr1243	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
vg1222100421	NA	1.01E-06	mr1498	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