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Detailed information for vg1215106306:

Variant ID: vg1215106306 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15106306
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGACACCATCATTATATTTTGCTTGTGCACATTTGATTGTTGTTTGAATATTGGTTTTTATCGCGTATTACAGAATTTGTATATCGGTTAGTCGTGAG[G/A]
CAACGTATGCAGCTTCCAGGAGGTGAAGGTTGATCAAGATTATATCAAGAATAAGAATTATCCTGAGCAGGCAAGTCATCACCCCATCCCTTGAGCATGT

Reverse complement sequence

ACATGCTCAAGGGATGGGGTGATGACTTGCCTGCTCAGGATAATTCTTATTCTTGATATAATCTTGATCAACCTTCACCTCCTGGAAGCTGCATACGTTG[C/T]
CTCACGACTAACCGATATACAAATTCTGTAATACGCGATAAAAACCAATATTCAAACAACAATCAAATGTGCACAAGCAAAATATAATGATGGTGTCGAA

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	76.60%	10.90%	2.64%	9.92%	NA
All Indica	2759	70.80%	9.90%	3.33%	15.98%	NA
All Japonica	1512	82.00%	15.10%	1.85%	1.06%	NA
Aus	269	97.80%	0.70%	0.00%	1.49%	NA
Indica I	595	92.30%	3.90%	2.02%	1.85%	NA
Indica II	465	60.20%	12.50%	4.73%	22.58%	NA
Indica III	913	64.50%	10.60%	3.07%	21.80%	NA
Indica Intermediate	786	68.10%	12.10%	3.82%	16.03%	NA
Temperate Japonica	767	91.40%	7.70%	0.52%	0.39%	NA
Tropical Japonica	504	70.40%	23.00%	4.56%	1.98%	NA
Japonica Intermediate	241	76.30%	22.00%	0.41%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	73.30%	12.20%	5.56%	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
vg1215106306	G -> DEL	N	N	silent_mutation	Average:44.667; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg1215106306	G -> A	LOC_Os12g26000-LOC_Os12g26010	intergenic_region ; MODIFIER	silent_mutation	Average:44.667; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215106306	5.76E-06	5.76E-06	mr1326	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
vg1215106306	NA	1.03E-06	mr1338	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
vg1215106306	8.20E-06	4.03E-07	mr1690	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
vg1215106306	NA	2.92E-06	mr1422_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
vg1215106306	NA	8.59E-06	mr1830_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