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Detailed information for vg0232704669:

Variant ID: vg0232704669 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32704669
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGTTGTTTACTGATTCATTTCTTGTGTAATAAAAAGCGCAGAATCATGCCTTGAATCCTATTAAAAAGAAAGATTCAAACAACGCAAAGCATTGTCCTA[T/A]
CGAGTTTTGGTGATTTTGCTCTTAGCGGACAGGATGCATTGGGTAACCGATTTCGTCCAAACCTTCAATAAAAGGCTACAATTCTAGGAGAGAGCTCATC

Reverse complement sequence

GATGAGCTCTCTCCTAGAATTGTAGCCTTTTATTGAAGGTTTGGACGAAATCGGTTACCCAATGCATCCTGTCCGCTAAGAGCAAAATCACCAAAACTCG[A/T]
TAGGACAATGCTTTGCGTTGTTTGAATCTTTCTTTTTAATAGGATTCAAGGCATGATTCTGCGCTTTTTATTACACAAGAAATGAATCAGTAAACAACTC

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	98.10%	1.80%	0.06%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	94.30%	5.60%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	88.30%	11.50%	0.20%	0.00%	NA
Japonica Intermediate	241	93.80%	5.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0232704669	T -> A	LOC_Os02g53440.1	upstream_gene_variant ; 4618.0bp to feature; MODIFIER	silent_mutation	Average:69.285; most accessible tissue: Zhenshan97 flower, score: 79.365	N	N	N	N
vg0232704669	T -> A	LOC_Os02g53450.2	downstream_gene_variant ; 15.0bp to feature; MODIFIER	silent_mutation	Average:69.285; most accessible tissue: Zhenshan97 flower, score: 79.365	N	N	N	N
vg0232704669	T -> A	LOC_Os02g53450-LOC_Os02g53470	intergenic_region ; MODIFIER	silent_mutation	Average:69.285; most accessible tissue: Zhenshan97 flower, score: 79.365	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232704669	NA	4.40E-06	mr1620	Jap_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
vg0232704669	1.76E-06	NA	mr1798_2	Jap_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