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Detailed information for vg1221525771:

Variant ID: vg1221525771 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21525771
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCATTTGTAAGTATTCTCAGGGCCATAAGTTCATCAGCAACCATCAACTAAGACAGAACATATTTTGATGCATTTGTGTAATGATTTGGAAGGACAATAT[C/T]
AAATATTCTAAGCAGTTTGCATAAACTCCCAACAAAAAAACATTTAGAGGAATGCAGCATTACTAACCATTCCAGGCATCTTGATCTCTTGTCTTGGTAG

Reverse complement sequence

CTACCAAGACAAGAGATCAAGATGCCTGGAATGGTTAGTAATGCTGCATTCCTCTAAATGTTTTTTTGTTGGGAGTTTATGCAAACTGCTTAGAATATTT[G/A]
ATATTGTCCTTCCAAATCATTACACAAATGCATCAAAATATGTTCTGTCTTAGTTGATGGTTGCTGATGAACTTATGGCCCTGAGAATACTTACAAATGC

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	94.10%	4.90%	0.02%	0.95%	NA
All Indica	2759	93.20%	5.10%	0.04%	1.59%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	68.80%	31.20%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	82.40%	17.40%	0.22%	0.00%	NA
Indica III	913	93.80%	3.70%	0.00%	2.52%	NA
Indica Intermediate	786	94.00%	3.30%	0.00%	2.67%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg1221525771	C -> DEL	N	N	silent_mutation	Average:70.606; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg1221525771	C -> T	LOC_Os12g35395.1	downstream_gene_variant ; 1006.0bp to feature; MODIFIER	silent_mutation	Average:70.606; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg1221525771	C -> T	LOC_Os12g35400.1	downstream_gene_variant ; 2946.0bp to feature; MODIFIER	silent_mutation	Average:70.606; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg1221525771	C -> T	LOC_Os12g35390-LOC_Os12g35395	intergenic_region ; MODIFIER	silent_mutation	Average:70.606; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221525771	6.39E-07	9.23E-09	mr1951	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