SHM Levels Comparisons

For the comparison of SHM levels, we used an IgG library from rhesus macaque D20, an animal that had not been used to generate the KIMDB database or the IMGT database. Three analyses were performed with the D20 IgG library. First, the library was assigned to the individualized D20 database to identify the appropriate germline assignment for each sequence read. For each assigned gene from D20 run, read identifiers were extracted and used to obtain SHM related values from the D20 IgG runs with KIMDB and IMGT as starting databases. All sequences assigned to a germline sequence in the initial individualized run were grouped into allele specific bins. The same allele specific binned sequences could then be traced in the subsequent KIMDB and IMGT assigned analyses, thereby enabling the SHM per gene to be determined based on the V_errors column of the filtered table output. Genes and their median V mutations, determined as number of differences reported by IgBLAST were compared to the closest IGHV allele in the database.