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Detailed information for vg1217863597:

Variant ID: vg1217863597 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17863597
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCGTGAAGATTTGTGAGCACTTGCATCATCTCCGGGAGTTCTTTGCTTCATTTTTTACTCTTGGAGGTTGAGGACTCCTAGGCGGCTAGGTGTCACTC[C/T]
CGAGCCACCGATCTACTTGTGGTTGCCGGGAGAAGTTTGTGAAGGTCGGATCTCACCTCCGAAAGGGAAGAGATACCCTTAATGGAAGGAGGAGTGCTTA

Reverse complement sequence

TAAGCACTCCTCCTTCCATTAAGGGTATCTCTTCCCTTTCGGAGGTGAGATCCGACCTTCACAAACTTCTCCCGGCAACCACAAGTAGATCGGTGGCTCG[G/A]
GAGTGACACCTAGCCGCCTAGGAGTCCTCAACCTCCAAGAGTAAAAAATGAAGCAAAGAACTCCCGGAGATGATGCAAGTGCTCACAAATCTTCACGAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.10%	7.20%	0.30%	29.45%	NA
All Indica	2759	57.60%	12.00%	0.43%	29.97%	NA
All Japonica	1512	75.30%	0.10%	0.07%	24.54%	NA
Aus	269	54.30%	0.00%	0.00%	45.72%	NA
Indica I	595	63.40%	28.20%	1.34%	7.06%	NA
Indica II	465	46.70%	10.10%	0.22%	43.01%	NA
Indica III	913	55.00%	3.30%	0.22%	41.51%	NA
Indica Intermediate	786	62.70%	10.90%	0.13%	26.21%	NA
Temperate Japonica	767	97.70%	0.10%	0.00%	2.22%	NA
Tropical Japonica	504	47.40%	0.20%	0.20%	52.18%	NA
Japonica Intermediate	241	62.20%	0.00%	0.00%	37.76%	NA
VI/Aromatic	96	46.90%	0.00%	0.00%	53.12%	NA
Intermediate	90	70.00%	6.70%	1.11%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217863597	C -> DEL	N	N	silent_mutation	Average:12.114; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg1217863597	C -> T	LOC_Os12g29874.1	upstream_gene_variant ; 558.0bp to feature; MODIFIER	silent_mutation	Average:12.114; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg1217863597	C -> T	LOC_Os12g29860.1	downstream_gene_variant ; 1394.0bp to feature; MODIFIER	silent_mutation	Average:12.114; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg1217863597	C -> T	LOC_Os12g29860-LOC_Os12g29874	intergenic_region ; MODIFIER	silent_mutation	Average:12.114; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217863597	3.38E-06	NA	mr1865	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