Calculating the rate of polymorphic Alu insertions
This protocol is extracted from research article:
Alu retrotransposons and COVID-19 susceptibility and morbidity
Hum Genomics, Jan 4, 2021; DOI: 10.1186/s40246-020-00299-9

All data of polymorphic Alu insertions were downloaded from the ALFRED database, except for Hispanic/Latino data of PGR, which was compiled from various sources including ALFRED [2527] (https://www.ncbi.nlm.nih.gov/snp/, accessed on September 5). Origin of genetic ancestry (OGA) is defined within the Allele Frequency Database, ALFRED [25]. The ALFRED database was chosen due to its inclusion of multiple samplings for the same OGA. The average rate in a given OGA (Table (Table1)1) was calculated as the weighted average. All calculations and data visualizations were conducted in R.

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