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Detailed information for vg1215632569:

Variant ID: vg1215632569 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15632569
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

ACGCACACAATAACTCCATCGTATGCCATATGGAATCTCCATCAACCACGTGCATCAACTCTAGCCTAAGTATCCCGCATGATCTCTGACCACAACGGAC[G/A]
TCGTCTTATCCCCAAGCCGACTCCTGGTCCATCACCGCAAATACTCTCCCGAGACATCGAGTCACCTACACATGGAACAAAGAAAGAAACCATATTCCGA

Reverse complement sequence

TCGGAATATGGTTTCTTTCTTTGTTCCATGTGTAGGTGACTCGATGTCTCGGGAGAGTATTTGCGGTGATGGACCAGGAGTCGGCTTGGGGATAAGACGA[C/T]
GTCCGTTGTGGTCAGAGATCATGCGGGATACTTAGGCTAGAGTTGATGCACGTGGTTGATGGAGATTCCATATGGCATACGATGGAGTTATTGTGTGCGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	30.80%	14.60%	6.35%	48.24%	NA
All Indica	2759	12.00%	7.10%	9.89%	71.04%	NA
All Japonica	1512	68.30%	20.90%	0.46%	10.38%	NA
Aus	269	15.60%	37.90%	5.58%	40.89%	NA
Indica I	595	14.50%	0.30%	10.42%	74.79%	NA
Indica II	465	7.70%	27.50%	5.38%	59.35%	NA
Indica III	913	10.80%	2.10%	12.81%	74.26%	NA
Indica Intermediate	786	14.00%	5.90%	8.78%	71.37%	NA
Temperate Japonica	767	91.70%	4.20%	0.65%	3.52%	NA
Tropical Japonica	504	35.50%	45.20%	0.40%	18.85%	NA
Japonica Intermediate	241	62.20%	23.20%	0.00%	14.52%	NA
VI/Aromatic	96	11.50%	60.40%	0.00%	28.12%	NA
Intermediate	90	44.40%	21.10%	5.56%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215632569	G -> DEL	N	N	silent_mutation	Average:14.704; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg1215632569	G -> A	LOC_Os12g26670.1	upstream_gene_variant ; 805.0bp to feature; MODIFIER	silent_mutation	Average:14.704; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg1215632569	G -> A	LOC_Os12g26660.1	downstream_gene_variant ; 3704.0bp to feature; MODIFIER	silent_mutation	Average:14.704; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg1215632569	G -> A	LOC_Os12g26680.1	downstream_gene_variant ; 4302.0bp to feature; MODIFIER	silent_mutation	Average:14.704; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg1215632569	G -> A	LOC_Os12g26670-LOC_Os12g26680	intergenic_region ; MODIFIER	silent_mutation	Average:14.704; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215632569	4.08E-06	2.87E-08	mr1855_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