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Detailed information for vg1225455213:

Variant ID: vg1225455213 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 25455213
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTATGACGCTGTTAACTTCTCAGATAATGTCTTATCATTCGTTTTATTCGAAAGTTTAGTATACATATGTAAAAGTATAAGTTAAAATTACGTTGAAAT[G/T]
AATTTATGGCTACATCGTATACAAATATAGAAGTATTTAATCTGTGTCTGAAATGATTTTCTGGCTACATTATGAAAAGAGAAGATTAAGAAAATACGCA

Reverse complement sequence

TGCGTATTTTCTTAATCTTCTCTTTTCATAATGTAGCCAGAAAATCATTTCAGACACAGATTAAATACTTCTATATTTGTATACGATGTAGCCATAAATT[C/A]
ATTTCAACGTAATTTTAACTTATACTTTTACATATGTATACTAAACTTTCGAATAAAACGAATGATAAGACATTATCTGAGAAGTTAACAGCGTCATACA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.80%	0.60%	0.61%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	96.30%	1.80%	1.92%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	96.00%	1.70%	2.35%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	90.50%	5.40%	4.15%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1225455213	G -> T	LOC_Os12g41090-LOC_Os12g41110	intergenic_region ; MODIFIER	silent_mutation	Average:57.841; most accessible tissue: Callus, score: 84.525	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1225455213	NA	4.10E-06	mr1280	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
vg1225455213	3.66E-06	NA	mr1563_2	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