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Detailed information for vg0410956225:

Variant ID: vg0410956225 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10956225
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAATAGAAAATGAGATATCGCCACAATTTTAATTTTTGTGGCAATTTATATAGTACATGGTACTTTTCACTATTTTTTGTTGCCACGATCAACAAATTC[G/A]
TTGCAATAAAAAATTTATCGTCTCATAATTTAACTTAATTTTTTCATATGGACACGGATTAAGACAAATTTAATATGGAAATTATAGCTCTCGACGATAT

Reverse complement sequence

ATATCGTCGAGAGCTATAATTTCCATATTAAATTTGTCTTAATCCGTGTCCATATGAAAAAATTAAGTTAAATTATGAGACGATAAATTTTTTATTGCAA[C/T]
GAATTTGTTGATCGTGGCAACAAAAAATAGTGAAAAGTACCATGTACTATATAAATTGCCACAAAAATTAAAATTGTGGCGATATCTCATTTTCTATTGC

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	85.70%	2.90%	4.76%	6.73%	NA
All Indica	2759	88.90%	4.90%	6.09%	0.18%	NA
All Japonica	1512	78.00%	0.00%	3.57%	18.45%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	58.20%	18.20%	23.70%	0.00%	NA
Indica II	465	98.30%	0.20%	0.86%	0.65%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	95.30%	1.50%	2.93%	0.25%	NA
Temperate Japonica	767	96.90%	0.00%	0.91%	2.22%	NA
Tropical Japonica	504	46.00%	0.00%	8.33%	45.63%	NA
Japonica Intermediate	241	84.60%	0.00%	2.07%	13.28%	NA
VI/Aromatic	96	71.90%	0.00%	1.04%	27.08%	NA
Intermediate	90	87.80%	1.10%	2.22%	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
vg0410956225	G -> DEL	N	N	silent_mutation	Average:21.72; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N
vg0410956225	G -> A	LOC_Os04g19640-LOC_Os04g19650	intergenic_region ; MODIFIER	silent_mutation	Average:21.72; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410956225	NA	7.84E-06	mr1679	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
vg0410956225	1.51E-06	NA	mr1804	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
vg0410956225	8.98E-06	1.51E-07	mr1804	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
vg0410956225	NA	7.15E-06	mr1184_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
vg0410956225	9.72E-06	9.71E-06	mr1284_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
vg0410956225	NA	3.62E-07	mr1531_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
vg0410956225	NA	8.17E-06	mr1556_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
vg0410956225	NA	6.69E-06	mr1636_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
vg0410956225	NA	1.48E-06	mr1683_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
vg0410956225	NA	4.36E-06	mr1759_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
vg0410956225	NA	6.44E-06	mr1759_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
vg0410956225	3.94E-06	3.94E-06	mr1764_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
vg0410956225	NA	2.06E-06	mr1838_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