V-J pairing analyses and somatic hypermutation assessment. V-J gene pairing for all IGL (A) and IGK (B) lymphoma clonotypes, in which a precise V and J gene assignment could be made by HighV-Quest. Frequency is the number of times a given V-J gene pair is present in a non-unique clonotype over the total number of times that V-J gene pair is seen across all the lymphoma clonotypes in the clinical database. Gray squares represent V-J gene combinations not present within the data set. For a large proportion of clonotypes, HighV-Quest was unable to differentiate between IGLJ2∗01, IGLJ3∗01, and sometimes IGLJ3∗02. These are grouped together in panel A when applicable as depicted along the x-axis. Likewise, when HighV-Quest was unable to differentiate between a V gene and its ‘D’ paralog, these were grouped together in panel B. (C) Boxplot of the percent identity to germline scores as determined by BLAT between heavy and light chain clonotypes. Clonotypes with no genomic match by BLAT to their respective heavy or light chain region were assigned a percent identity score of zero.