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Detailed information for vg1227007533:

Variant ID: vg1227007533 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 27007533
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTACTTTTTCTACTGTAAAATTGGTATCTCTTGATATTAGATACCAAGAGATACTAAATTTACATTAAATGTTTGGTTACTCATACTAATATCAAAGTAA[T/C]
GCAAGCTATAGCTAACATATAGTTGTTCGATCTGCGTCAATTAATTAATTTATTACAAGTAGTAATTATTATTAGCAGAATTGGTAGAGATATCCATGAT

Reverse complement sequence

ATCATGGATATCTCTACCAATTCTGCTAATAATAATTACTACTTGTAATAAATTAATTAATTGACGCAGATCGAACAACTATATGTTAGCTATAGCTTGC[A/G]
TTACTTTGATATTAGTATGAGTAACCAAACATTTAATGTAAATTTAGTATCTCTTGGTATCTAATATCAAGAGATACCAATTTTACAGTAGAAAAAGTAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.90%	1.90%	0.21%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.07%	0.00%	NA
All Japonica	1512	93.70%	5.80%	0.53%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	90.90%	8.20%	0.91%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	90.00%	9.50%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1227007533	T -> C	LOC_Os12g43530.1	downstream_gene_variant ; 53.0bp to feature; MODIFIER	silent_mutation	Average:54.6; most accessible tissue: Callus, score: 81.241	N	N	N	N
vg1227007533	T -> C	LOC_Os12g43520-LOC_Os12g43530	intergenic_region ; MODIFIER	silent_mutation	Average:54.6; most accessible tissue: Callus, score: 81.241	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1227007533	6.02E-07	6.02E-07	mr1935	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