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Detailed information for vg1215721018:

Variant ID: vg1215721018 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15721018
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAGAATTACTTTAACTTTTATTGATCTTAACTTGGTTTCATTATTACAAAACTGAAGACTCTCACACCACTAAACTCAACAACTTCCTAATACTCAAAA[A/G]
CAAACAAACGCATGCACTTACATCCCACCACTGATGTAAATCACATGCGAGACACACACAAGCAAACTTAAAACAAGCAAACTAACACAACGATCTAAGA

Reverse complement sequence

TCTTAGATCGTTGTGTTAGTTTGCTTGTTTTAAGTTTGCTTGTGTGTGTCTCGCATGTGATTTACATCAGTGGTGGGATGTAAGTGCATGCGTTTGTTTG[T/C]
TTTTGAGTATTAGGAAGTTGTTGAGTTTAGTGGTGTGAGAGTCTTCAGTTTTGTAATAATGAAACCAAGTTAAGATCAATAAAAGTTAAAGTAATTCTCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.70%	0.10%	30.05%	31.17%	NA
All Indica	2759	19.40%	0.20%	39.91%	40.56%	NA
All Japonica	1512	71.00%	0.00%	12.43%	16.60%	NA
Aus	269	52.80%	0.00%	25.65%	21.56%	NA
Indica I	595	26.60%	0.20%	19.66%	53.61%	NA
Indica II	465	26.90%	0.20%	24.52%	48.39%	NA
Indica III	913	7.60%	0.00%	66.16%	26.29%	NA
Indica Intermediate	786	23.20%	0.40%	33.84%	42.62%	NA
Temperate Japonica	767	93.70%	0.00%	1.69%	4.56%	NA
Tropical Japonica	504	36.30%	0.00%	27.58%	36.11%	NA
Japonica Intermediate	241	71.00%	0.00%	14.94%	14.11%	NA
VI/Aromatic	96	35.40%	0.00%	39.58%	25.00%	NA
Intermediate	90	50.00%	0.00%	26.67%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215721018	A -> DEL	N	N	silent_mutation	Average:11.59; most accessible tissue: Callus, score: 26.308	N	N	N	N
vg1215721018	A -> G	LOC_Os12g26840.1	downstream_gene_variant ; 4371.0bp to feature; MODIFIER	silent_mutation	Average:11.59; most accessible tissue: Callus, score: 26.308	N	N	N	N
vg1215721018	A -> G	LOC_Os12g26830.1	intron_variant ; MODIFIER	silent_mutation	Average:11.59; most accessible tissue: Callus, score: 26.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215721018	NA	3.15E-06	mr1013_2	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
vg1215721018	NA	4.70E-06	mr1031_2	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
vg1215721018	NA	5.82E-06	mr1577_2	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