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Detailed information for vg1215215031:

Variant ID: vg1215215031 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15215031
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCATTGTCTAAAAGAAAAATAATACAGGGCGAAAACCGGCCCAATTAATCTACACTACTACATATTACAGTACATAGTACTTCTTCCGTTTCACAATATA[A/T]
GTTATTCTAGCATTTCCCACGTTCATATGGATGTTCAATATGAATGTGGAAAATGCTAGAATGACTTATATTGTGAAACGGAGGGAGTATATATACACAT

Reverse complement sequence

ATGTGTATATATACTCCCTCCGTTTCACAATATAAGTCATTCTAGCATTTTCCACATTCATATTGAACATCCATATGAACGTGGGAAATGCTAGAATAAC[T/A]
TATATTGTGAAACGGAAGAAGTACTATGTACTGTAATATGTAGTAGTGTAGATTAATTGGGCCGGTTTTCGCCCTGTATTATTTTTCTTTTAGACAATGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.70%	2.10%	1.33%	5.88%	NA
All Indica	2759	89.80%	0.00%	0.33%	9.86%	NA
All Japonica	1512	90.00%	6.40%	3.51%	0.07%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	98.80%	0.00%	0.17%	1.01%	NA
Indica II	465	97.20%	0.00%	0.00%	2.80%	NA
Indica III	913	81.30%	0.00%	0.66%	18.07%	NA
Indica Intermediate	786	88.40%	0.10%	0.25%	11.20%	NA
Temperate Japonica	767	85.50%	8.30%	6.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.20%	0.20%	NA
Japonica Intermediate	241	84.60%	13.30%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	0.00%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215215031	A -> DEL	N	N	silent_mutation	Average:41.667; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N
vg1215215031	A -> T	LOC_Os12g26120-LOC_Os12g26140	intergenic_region ; MODIFIER	silent_mutation	Average:41.667; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215215031	NA	3.48E-09	mr1100_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
vg1215215031	NA	7.18E-07	mr1203_2	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
vg1215215031	NA	1.45E-06	mr1613_2	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
vg1215215031	NA	4.90E-06	mr1619_2	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
vg1215215031	NA	2.33E-08	mr1913_2	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