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Detailed information for vg0403835689:

Variant ID: vg0403835689 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3835689
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, A: 0.16, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:

AATGCCAGGACTCTGAAGCCAATACTGACTCTAAGCCGATGATTACTCTGGGCTTACCAAATTTCACTGATAGCAACATGTTAGACCTTGTTTGGCTAAT[T/A]
CCACCCACAAAGGTCTCAATCCCCTCCTTGTGGGAATAACCGAACAAGACCTTATATATGCCATAAAAGAGTCGCAATTAGGGATGGCAACGGGACTGGG

Reverse complement sequence

CCCAGTCCCGTTGCCATCCCTAATTGCGACTCTTTTATGGCATATATAAGGTCTTGTTCGGTTATTCCCACAAGGAGGGGATTGAGACCTTTGTGGGTGG[A/T]
ATTAGCCAAACAAGGTCTAACATGTTGCTATCAGTGAAATTTGGTAAGCCCAGAGTAATCATCGGCTTAGAGTCAGTATTGGCTTCAGAGTCCTGGCATT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.30%	13.50%	1.54%	25.65%	NA
All Indica	2759	61.40%	4.90%	0.69%	33.06%	NA
All Japonica	1512	55.20%	31.20%	0.40%	13.29%	NA
Aus	269	44.20%	8.20%	15.61%	31.97%	NA
Indica I	595	98.50%	1.00%	0.00%	0.50%	NA
Indica II	465	69.50%	10.30%	0.65%	19.57%	NA
Indica III	913	33.30%	1.90%	0.99%	63.86%	NA
Indica Intermediate	786	61.10%	8.10%	0.89%	29.90%	NA
Temperate Japonica	767	47.50%	51.00%	0.00%	1.56%	NA
Tropical Japonica	504	59.70%	9.10%	0.40%	30.75%	NA
Japonica Intermediate	241	70.10%	14.10%	1.66%	14.11%	NA
VI/Aromatic	96	94.80%	3.10%	1.04%	1.04%	NA
Intermediate	90	74.40%	6.70%	5.56%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403835689	T -> DEL	N	N	silent_mutation	Average:58.486; most accessible tissue: Minghui63 young leaf, score: 76.385	N	N	N	N
vg0403835689	T -> A	LOC_Os04g07230.1	upstream_gene_variant ; 374.0bp to feature; MODIFIER	silent_mutation	Average:58.486; most accessible tissue: Minghui63 young leaf, score: 76.385	N	N	N	N
vg0403835689	T -> A	LOC_Os04g07220-LOC_Os04g07230	intergenic_region ; MODIFIER	silent_mutation	Average:58.486; most accessible tissue: Minghui63 young leaf, score: 76.385	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403835689	NA	9.40E-06	mr1582_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
vg0403835689	4.39E-08	2.42E-09	mr1807_2	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