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Detailed information for vg1221501463:

Variant ID: vg1221501463 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21501463
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAACCGTTTAAAAATATGTGTTAACGGGGAATAAGAAAAATTAAAGTTTGGAGTCCAAGGAAGATAGTATCGGCAATAACAAAAGGAAAAAGTACAAATT[C/A]
CCCCGAACTATCGCGGTCGACCAAATTACACCTCTGAACCCGAAAACCAGTCATCGTTCACCTTGAATTTTTAATACCGGACAAATTACCTCCGTCGACC

Reverse complement sequence

GGTCGACGGAGGTAATTTGTCCGGTATTAAAAATTCAAGGTGAACGATGACTGGTTTTCGGGTTCAGAGGTGTAATTTGGTCGACCGCGATAGTTCGGGG[G/T]
AATTTGTACTTTTTCCTTTTGTTATTGCCGATACTATCTTCCTTGGACTCCAAACTTTAATTTTTCTTATTCCCCGTTAACACATATTTTTAAACGGTTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.90%	7.40%	3.47%	20.25%	NA
All Indica	2759	57.70%	12.10%	5.44%	24.76%	NA
All Japonica	1512	99.10%	0.20%	0.00%	0.66%	NA
Aus	269	12.30%	1.50%	4.09%	82.16%	NA
Indica I	595	66.70%	13.80%	0.67%	18.82%	NA
Indica II	465	70.10%	6.50%	15.27%	8.17%	NA
Indica III	913	40.30%	13.00%	3.50%	43.15%	NA
Indica Intermediate	786	63.60%	13.20%	5.47%	17.68%	NA
Temperate Japonica	767	99.20%	0.30%	0.00%	0.52%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	98.30%	0.40%	0.00%	1.24%	NA
VI/Aromatic	96	62.50%	1.00%	0.00%	36.46%	NA
Intermediate	90	78.90%	8.90%	3.33%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221501463	C -> DEL	N	N	silent_mutation	Average:61.677; most accessible tissue: Callus, score: 78.877	N	N	N	N
vg1221501463	C -> A	LOC_Os12g35360.1	upstream_gene_variant ; 619.0bp to feature; MODIFIER	silent_mutation	Average:61.677; most accessible tissue: Callus, score: 78.877	N	N	N	N
vg1221501463	C -> A	LOC_Os12g35370.1	upstream_gene_variant ; 4132.0bp to feature; MODIFIER	silent_mutation	Average:61.677; most accessible tissue: Callus, score: 78.877	N	N	N	N
vg1221501463	C -> A	LOC_Os12g35364.1	downstream_gene_variant ; 2154.0bp to feature; MODIFIER	silent_mutation	Average:61.677; most accessible tissue: Callus, score: 78.877	N	N	N	N
vg1221501463	C -> A	LOC_Os12g35360-LOC_Os12g35364	intergenic_region ; MODIFIER	silent_mutation	Average:61.677; most accessible tissue: Callus, score: 78.877	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221501463	NA	3.04E-06	mr1062	Ind_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
vg1221501463	NA	1.09E-06	mr1195	Ind_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
vg1221501463	NA	7.55E-06	mr1541	Ind_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
vg1221501463	NA	2.73E-06	mr1748	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
vg1221501463	2.53E-06	2.53E-06	mr1748	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