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Detailed information for vg0233523559:

Variant ID: vg0233523559 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 33523559
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCATAATTTAGAGATTCAAAATAGATGTCTTTTGAGTAAATGGTTGTTCAAGTTAATAAATGAAAATGGTGTTTGGCAAGACTTATTGAAGAGAAAGTAT[C/T]
TTTATAATAAGTCTATCACCCAAGTTGACAGGAAACAAGGTGACTCCCATTTTTGGTCAGGACTCATGAAAGTCAAAAAAAACTTTCTTAACTATGGGTT

Reverse complement sequence

AACCCATAGTTAAGAAAGTTTTTTTTGACTTTCATGAGTCCTGACCAAAAATGGGAGTCACCTTGTTTCCTGTCAACTTGGGTGATAGACTTATTATAAA[G/A]
ATACTTTCTCTTCAATAAGTCTTGCCAAACACCATTTTCATTTATTAACTTGAACAACCATTTACTCAAAAGACATCTATTTTGAATCTCTAAATTATGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.60%	7.20%	40.80%	14.45%	NA
All Indica	2759	5.20%	3.20%	67.20%	24.39%	NA
All Japonica	1512	98.60%	0.10%	0.93%	0.33%	NA
Aus	269	2.20%	83.60%	14.13%	0.00%	NA
Indica I	595	4.90%	0.20%	52.61%	42.35%	NA
Indica II	465	6.90%	0.40%	57.20%	35.48%	NA
Indica III	913	4.20%	4.60%	82.91%	8.32%	NA
Indica Intermediate	786	5.60%	5.60%	65.90%	22.90%	NA
Temperate Japonica	767	98.30%	0.00%	1.43%	0.26%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	0.80%	1.24%	1.24%	NA
VI/Aromatic	96	84.40%	13.50%	2.08%	0.00%	NA
Intermediate	90	61.10%	11.10%	22.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0233523559	C -> T	LOC_Os02g54740.1	downstream_gene_variant ; 349.0bp to feature; MODIFIER	silent_mutation	Average:12.506; most accessible tissue: Callus, score: 22.935	N	N	N	N
vg0233523559	C -> T	LOC_Os02g54750.1	downstream_gene_variant ; 2496.0bp to feature; MODIFIER	silent_mutation	Average:12.506; most accessible tissue: Callus, score: 22.935	N	N	N	N
vg0233523559	C -> T	LOC_Os02g54740-LOC_Os02g54750	intergenic_region ; MODIFIER	silent_mutation	Average:12.506; most accessible tissue: Callus, score: 22.935	N	N	N	N
vg0233523559	C -> DEL	N	N	silent_mutation	Average:12.506; most accessible tissue: Callus, score: 22.935	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0233523559	3.61E-06	NA	mr1170	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