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Detailed information for vg1217491800:

Variant ID: vg1217491800 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17491800
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

GAAATGCTTGTTGGTATTTCTTAACGTCATTACTAGAAATATAATTCCCAGCAATGGCGCAGAAATACCTCTGGTATATTATGGTTACAGAGTTCATCCG[C/T]
AAGCGCACGGATATACCATTGTAGCATTTCACCCGAGAGTATTCCAAGGGTATCGTATTTATTTTATCCCGTGGAAAGATCATGTAGAGAGAACTTGATT

Reverse complement sequence

AATCAAGTTCTCTCTACATGATCTTTCCACGGGATAAAATAAATACGATACCCTTGGAATACTCTCGGGTGAAATGCTACAATGGTATATCCGTGCGCTT[G/A]
CGGATGAACTCTGTAACCATAATATACCAGAGGTATTTCTGCGCCATTGCTGGGAATTATATTTCTAGTAATGACGTTAAGAAATACCAACAAGCATTTC

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	92.00%	5.10%	1.14%	1.71%	NA
All Indica	2759	97.20%	2.10%	0.58%	0.14%	NA
All Japonica	1512	84.90%	9.90%	0.26%	5.03%	NA
Aus	269	87.40%	0.40%	12.27%	0.00%	NA
Indica I	595	97.10%	0.00%	2.69%	0.17%	NA
Indica II	465	90.50%	9.50%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.10%	0.00%	0.38%	NA
Temperate Japonica	767	90.20%	0.10%	0.39%	9.26%	NA
Tropical Japonica	504	72.80%	27.00%	0.20%	0.00%	NA
Japonica Intermediate	241	92.90%	5.00%	0.00%	2.07%	NA
VI/Aromatic	96	72.90%	26.00%	1.04%	0.00%	NA
Intermediate	90	87.80%	11.10%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217491800	C -> DEL	N	N	silent_mutation	Average:27.442; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg1217491800	C -> T	LOC_Os12g29440.1	upstream_gene_variant ; 978.0bp to feature; MODIFIER	silent_mutation	Average:27.442; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg1217491800	C -> T	LOC_Os12g29434.1	downstream_gene_variant ; 4667.0bp to feature; MODIFIER	silent_mutation	Average:27.442; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg1217491800	C -> T	LOC_Os12g29440-LOC_Os12g29450	intergenic_region ; MODIFIER	silent_mutation	Average:27.442; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217491800	NA	3.89E-09	mr1364	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
vg1217491800	NA	1.61E-09	mr1443	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
vg1217491800	NA	6.72E-07	mr1471	Jap_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