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Detailed information for vg0402380608:

Variant ID: vg0402380608 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2380608
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.34, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTATACTTCGTGGCTCCGAGTTGCAAGCGCTTTGCTTCTGCTTCGTCTTCCGGAAGCTAGCCAGTTTCAAGGTGTTTTACAAACGGGGTTCGCCAGTC[G/A]
TATGGGTCTTCGCCCAGTTTCACCTGGTCGATTGCCATGATCTCCAAGCTATCCATGGGCACACTTGGTGCATGCAGGACTTCGAAAAAGATGCCAGGCG

Reverse complement sequence

CGCCTGGCATCTTTTTCGAAGTCCTGCATGCACCAAGTGTGCCCATGGATAGCTTGGAGATCATGGCAATCGACCAGGTGAAACTGGGCGAAGACCCATA[C/T]
GACTGGCGAACCCCGTTTGTAAAACACCTTGAAACTGGCTAGCTTCCGGAAGACGAAGCAGAAGCAAAGCGCTTGCAACTCGGAGCCACGAAGTATAAGA

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	27.90%	25.10%	6.03%	40.94%	NA
All Indica	2759	41.40%	5.90%	7.39%	45.31%	NA
All Japonica	1512	2.00%	61.60%	3.97%	32.47%	NA
Aus	269	43.10%	10.80%	5.58%	40.52%	NA
Indica I	595	20.30%	8.70%	5.04%	65.88%	NA
Indica II	465	49.00%	3.40%	5.81%	41.72%	NA
Indica III	913	51.40%	3.50%	9.64%	35.49%	NA
Indica Intermediate	786	41.10%	8.10%	7.51%	43.26%	NA
Temperate Japonica	767	0.30%	87.60%	1.30%	10.82%	NA
Tropical Japonica	504	4.20%	33.50%	7.14%	55.16%	NA
Japonica Intermediate	241	2.90%	37.30%	5.81%	53.94%	NA
VI/Aromatic	96	5.20%	34.40%	3.12%	57.29%	NA
Intermediate	90	30.00%	33.30%	3.33%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402380608	G -> DEL	N	N	silent_mutation	Average:19.818; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0402380608	G -> A	LOC_Os04g04930.1	downstream_gene_variant ; 2810.0bp to feature; MODIFIER	silent_mutation	Average:19.818; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0402380608	G -> A	LOC_Os04g04940.1	intron_variant ; MODIFIER	silent_mutation	Average:19.818; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402380608	NA	5.53E-09	mr1403	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
vg0402380608	NA	2.93E-06	mr1414	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
vg0402380608	NA	8.30E-06	mr1830	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
vg0402380608	NA	5.92E-11	mr1846	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
vg0402380608	NA	7.60E-09	mr1846	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
vg0402380608	NA	4.79E-07	mr1830_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
vg0402380608	NA	5.82E-22	mr1846_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
vg0402380608	NA	7.20E-19	mr1846_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