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Detailed information for vg0412755389:

Variant ID: vg0412755389 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12755389
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCATTTATGTTTTATGTATTTCCAGAAATTTATTTATGACCTTTCTTAGCCATTAAAAATTGCTGGAAAATTATGGTCAATTATTTGATCACTCAGAAA[A/T]
TTATTTCTAGTTAAATGGAACCAACAGGAAGTTTAGCTAGAAAGAAATTAATGATATGATATTATATTTGACCAATGTTAATATGATTTCATGTCAATAT

Reverse complement sequence

ATATTGACATGAAATCATATTAACATTGGTCAAATATAATATCATATCATTAATTTCTTTCTAGCTAAACTTCCTGTTGGTTCCATTTAACTAGAAATAA[T/A]
TTTCTGAGTGATCAAATAATTGACCATAATTTTCCAGCAATTTTTAATGGCTAAGAAAGGTCATAAATAAATTTCTGGAAATACATAAAACATAAATGGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.20%	0.10%	2.03%	52.62%	NA
All Indica	2759	18.10%	0.20%	3.08%	78.62%	NA
All Japonica	1512	98.10%	0.00%	0.33%	1.59%	NA
Aus	269	3.30%	0.40%	1.49%	94.80%	NA
Indica I	595	6.70%	0.00%	2.69%	90.59%	NA
Indica II	465	21.30%	0.20%	1.51%	76.99%	NA
Indica III	913	26.00%	0.10%	3.40%	70.54%	NA
Indica Intermediate	786	15.80%	0.40%	3.94%	79.90%	NA
Temperate Japonica	767	98.20%	0.00%	0.39%	1.43%	NA
Tropical Japonica	504	99.00%	0.00%	0.20%	0.79%	NA
Japonica Intermediate	241	95.90%	0.00%	0.41%	3.73%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	62.20%	0.00%	2.22%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412755389	A -> DEL	N	N	silent_mutation	Average:7.02; most accessible tissue: Callus, score: 22.586	N	N	N	N
vg0412755389	A -> T	LOC_Os04g22510.1	upstream_gene_variant ; 4723.0bp to feature; MODIFIER	silent_mutation	Average:7.02; most accessible tissue: Callus, score: 22.586	N	N	N	N
vg0412755389	A -> T	LOC_Os04g22510-LOC_Os04g22520	intergenic_region ; MODIFIER	silent_mutation	Average:7.02; most accessible tissue: Callus, score: 22.586	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412755389	4.13E-07	2.57E-08	mr1910	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
vg0412755389	6.49E-07	6.49E-07	mr1910	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
vg0412755389	NA	4.86E-06	mr1955	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