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Detailed information for vg1217503845:

Variant ID: vg1217503845 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17503845
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTGCTTAGCTCCTGTGCAAGTCCAAATCTTAGTGAGATGCAGGCATGCCAGTCAGTTTGGTCCTGCAACTAACAAGATATGCAAATAGTAGATCAAAA[C/G]
AGCCGATCGGCTGACAAGCCGATGGAGTAGTTCCAGCCGATAGCCGATAATAGCCAATGCCGATACCAGCCGATAGCGATAGGGTTTTGTGCTATCAGCT

Reverse complement sequence

AGCTGATAGCACAAAACCCTATCGCTATCGGCTGGTATCGGCATTGGCTATTATCGGCTATCGGCTGGAACTACTCCATCGGCTTGTCAGCCGATCGGCT[G/C]
TTTTGATCTACTATTTGCATATCTTGTTAGTTGCAGGACCAAACTGACTGGCATGCCTGCATCTCACTAAGATTTGGACTTGCACAGGAGCTAAGCAGAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.50%	5.20%	1.35%	6.94%	NA
All Indica	2759	85.70%	8.80%	2.17%	3.26%	NA
All Japonica	1512	92.30%	0.10%	0.07%	7.54%	NA
Aus	269	53.90%	0.00%	0.74%	45.35%	NA
Indica I	595	72.60%	11.40%	7.23%	8.74%	NA
Indica II	465	90.80%	8.20%	0.65%	0.43%	NA
Indica III	913	94.20%	5.10%	0.11%	0.55%	NA
Indica Intermediate	786	82.80%	11.60%	1.65%	3.94%	NA
Temperate Japonica	767	86.70%	0.10%	0.13%	13.04%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	0.00%	0.00%	5.81%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	2.20%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217503845	C -> DEL	N	N	silent_mutation	Average:42.407; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1217503845	C -> G	LOC_Os12g29450.1	upstream_gene_variant ; 3525.0bp to feature; MODIFIER	silent_mutation	Average:42.407; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1217503845	C -> G	LOC_Os12g29450-LOC_Os12g29470	intergenic_region ; MODIFIER	silent_mutation	Average:42.407; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217503845	4.95E-06	3.93E-06	mr1745	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
vg1217503845	4.07E-07	4.07E-07	mr1778	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
vg1217503845	4.85E-06	NA	mr1973	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