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Detailed information for vg1205317195:

Variant ID: vg1205317195 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5317195
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.05, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCGACATTTATCAGTAAGAATTTATCTGCAGAATTCAAAACCAAGTTAATAGAGCTATTGAAAGAATATAGAGATTGCTTTGCTTGGGAATATTATGA[A/G]
ATGCCAGGACTCAGCCGATCGATTGTTGAACATCGGCTTCCTATTAAGCCAGGATATAATCCACATCAGCAACCACCTAGGAGGTGCAAAGCCGATATGT

Reverse complement sequence

ACATATCGGCTTTGCACCTCCTAGGTGGTTGCTGATGTGGATTATATCCTGGCTTAATAGGAAGCCGATGTTCAACAATCGATCGGCTGAGTCCTGGCAT[T/C]
TCATAATATTCCCAAGCAAAGCAATCTCTATATTCTTTCAATAGCTCTATTAACTTGGTTTTGAATTCTGCAGATAAATTCTTACTGATAAATGTCGGCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.10%	0.90%	1.29%	56.71%	NA
All Indica	2759	10.60%	1.30%	1.88%	86.19%	NA
All Japonica	1512	94.70%	0.00%	0.13%	5.16%	NA
Aus	269	23.00%	1.10%	2.23%	73.61%	NA
Indica I	595	13.40%	1.30%	2.52%	82.69%	NA
Indica II	465	12.70%	1.50%	1.29%	84.52%	NA
Indica III	913	5.50%	0.30%	0.99%	93.21%	NA
Indica Intermediate	786	13.10%	2.40%	2.80%	81.68%	NA
Temperate Japonica	767	96.50%	0.00%	0.00%	3.52%	NA
Tropical Japonica	504	95.00%	0.00%	0.00%	4.96%	NA
Japonica Intermediate	241	88.40%	0.00%	0.83%	10.79%	NA
VI/Aromatic	96	93.80%	2.10%	0.00%	4.17%	NA
Intermediate	90	74.40%	0.00%	1.11%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205317195	A -> DEL	N	N	silent_mutation	Average:17.12; most accessible tissue: Callus, score: 48.02	N	N	N	N
vg1205317195	A -> G	LOC_Os12g10030.1	upstream_gene_variant ; 1163.0bp to feature; MODIFIER	silent_mutation	Average:17.12; most accessible tissue: Callus, score: 48.02	N	N	N	N
vg1205317195	A -> G	LOC_Os12g10040.1	upstream_gene_variant ; 273.0bp to feature; MODIFIER	silent_mutation	Average:17.12; most accessible tissue: Callus, score: 48.02	N	N	N	N
vg1205317195	A -> G	LOC_Os12g10050.1	upstream_gene_variant ; 4961.0bp to feature; MODIFIER	silent_mutation	Average:17.12; most accessible tissue: Callus, score: 48.02	N	N	N	N
vg1205317195	A -> G	LOC_Os12g10030-LOC_Os12g10040	intergenic_region ; MODIFIER	silent_mutation	Average:17.12; most accessible tissue: Callus, score: 48.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205317195	2.11E-07	3.18E-09	mr1301	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
vg1205317195	NA	3.50E-11	mr1713	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