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Detailed information for vg0224385795:

Variant ID: vg0224385795 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24385795
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.31, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

AGTCTTTCAAAGTCTGAAGATAACTAGCTATTTAATAAATTTTAAGCAAAATCATATTAAAAATAGATAATTTTGTATGAATGCTAGCCACGCAATTGCG[C/T]
GAGCAACCCAGTTAGTTTATAAAACCTAGTCACTTTGGGTCCTTACACGGTTTTGACCGCGGTTTTATCTGACGTGTCGGCTGAGTTAGCATGAGACCCC

Reverse complement sequence

GGGGTCTCATGCTAACTCAGCCGACACGTCAGATAAAACCGCGGTCAAAACCGTGTAAGGACCCAAAGTGACTAGGTTTTATAAACTAACTGGGTTGCTC[G/A]
CGCAATTGCGTGGCTAGCATTCATACAAAATTATCTATTTTTAATATGATTTTGCTTAAAATTTATTAAATAGCTAGTTATCTTCAGACTTTGAAAGACT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.50%	27.30%	1.12%	23.13%	NA
All Indica	2759	48.40%	30.00%	1.27%	20.33%	NA
All Japonica	1512	48.90%	22.00%	0.20%	28.97%	NA
Aus	269	50.90%	30.50%	4.83%	13.75%	NA
Indica I	595	17.00%	37.50%	2.86%	42.69%	NA
Indica II	465	57.00%	34.40%	0.43%	8.17%	NA
Indica III	913	58.30%	23.10%	0.66%	17.96%	NA
Indica Intermediate	786	55.50%	29.90%	1.27%	13.36%	NA
Temperate Japonica	767	40.80%	23.10%	0.39%	35.72%	NA
Tropical Japonica	504	63.90%	24.00%	0.00%	12.10%	NA
Japonica Intermediate	241	43.20%	14.10%	0.00%	42.74%	NA
VI/Aromatic	96	38.50%	18.80%	2.08%	40.62%	NA
Intermediate	90	50.00%	30.00%	0.00%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224385795	C -> T	LOC_Os02g40270.1	upstream_gene_variant ; 3122.0bp to feature; MODIFIER	silent_mutation	Average:42.027; most accessible tissue: Callus, score: 66.021	N	N	N	N
vg0224385795	C -> T	LOC_Os02g40280.1	downstream_gene_variant ; 4936.0bp to feature; MODIFIER	silent_mutation	Average:42.027; most accessible tissue: Callus, score: 66.021	N	N	N	N
vg0224385795	C -> T	LOC_Os02g40270-LOC_Os02g40280	intergenic_region ; MODIFIER	silent_mutation	Average:42.027; most accessible tissue: Callus, score: 66.021	N	N	N	N
vg0224385795	C -> DEL	N	N	silent_mutation	Average:42.027; most accessible tissue: Callus, score: 66.021	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224385795	NA	6.60E-07	mr1125_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