The vivaxGEN-geo tool uses Plasmodium vivax genotyping data generated at a selection of SNP barcodes to predict the country of origin of a given sample. Country predictions are derived using a likelihood classifier. The likelihood classifier was trained using data from the following countries: Afghanistan, Bangladesh, Bhutan, Brazil, Cambodia, China, Colombia, Ethiopia, India, Indonesia, Iran, Madagascar, Malaysia, Mexico, Myanmar, Papua New Guinea, Peru, Sudan, Thailand and Vietnam.
For more information, please read the reference (Trimarsanto, 2019).
All SNP positions are based on PvP01 reference genome (Auburn, 2016):
- SNP-28: 28 SNPs determined by Hierarchical FST method (Trimarsanto, 2019)
- SNP-28+Broad (65 SNPs): combination of SNP-28 and 37 SNPs from Broad barcodes (Baniecki, 2015)
- Broad-38 (SPOTMalaria order): 38 SNPs from Broad barcodes used by SPOTMalaria project as reported in the project report card order
- Broad-38 (positional order): 38 SNPs from Broad barcodes used by SPOTMalaria project in chromosomal positional order
- Broad-37: 37 high-quality Broad barcode SNPs from P vivax WGS set data used in (Trimarsanto, 2019)