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Detailed information for vg1224308470:

Variant ID: vg1224308470 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24308470
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGTGAAGCTTAATCTATACTACTTTAAATATTAATAGTGGTGGCTGCAGTAAATCTACCATCACCATCCTCTTACTGATGTGTGGGCTCACAATGTGT[A/G]
TGTCAAAGAAACATAGCTCTATGTCTCATGACTCTGGCTAACTAGGTAAGAATCGAAAATATTTATGACAAAAAATGATTGGAGAGCTAAATATTTTTAG

Reverse complement sequence

CTAAAAATATTTAGCTCTCCAATCATTTTTTGTCATAAATATTTTCGATTCTTACCTAGTTAGCCAGAGTCATGAGACATAGAGCTATGTTTCTTTGACA[T/C]
ACACATTGTGAGCCCACACATCAGTAAGAGGATGGTGATGGTAGATTTACTGCAGCCACCACTATTAATATTTAAAGTAGTATAGATTAAGCTTCACTGT

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	70.70%	5.40%	1.23%	22.70%	NA
All Indica	2759	50.60%	9.20%	2.07%	38.17%	NA
All Japonica	1512	99.40%	0.10%	0.00%	0.53%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	37.50%	33.10%	0.67%	28.74%	NA
Indica II	465	51.00%	1.10%	1.29%	46.67%	NA
Indica III	913	67.00%	0.10%	1.86%	31.00%	NA
Indica Intermediate	786	41.10%	6.50%	3.82%	48.60%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	0.00%	1.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1224308470	A -> DEL	N	N	silent_mutation	Average:40.139; most accessible tissue: Callus, score: 70.182	N	N	N	N
vg1224308470	A -> G	LOC_Os12g39440-LOC_Os12g39450	intergenic_region ; MODIFIER	silent_mutation	Average:40.139; most accessible tissue: Callus, score: 70.182	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224308470	NA	6.93E-08	mr1038	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
vg1224308470	NA	3.57E-07	mr1038	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
vg1224308470	NA	1.22E-08	mr1389	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
vg1224308470	NA	1.30E-07	mr1389	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
vg1224308470	NA	1.01E-08	mr1571	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
vg1224308470	NA	3.98E-06	mr1974	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
vg1224308470	NA	6.37E-06	mr1974	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
vg1224308470	NA	2.14E-08	mr1038_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
vg1224308470	NA	1.77E-07	mr1038_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
vg1224308470	NA	3.46E-06	mr1170_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
vg1224308470	NA	1.54E-07	mr1389_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
vg1224308470	NA	2.06E-07	mr1389_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
vg1224308470	NA	6.88E-07	mr1571_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
vg1224308470	NA	3.59E-06	mr1637_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