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Background  The Jurkat cell line has an extensive history as a model of T cell signaling. But at the turn of the 21st century, some expression irregularities were observed, raising doubts about how closely the cell line paralleled normal human T cells. While numerous expression deficiencies have been described in Jurkat, genetic explanations have only been provided for a handful of defects.    Results  Here, we report a comprehensive catolog of genomic variation in the Jurkat cell line based on whole-genome sequencing. With this list of all detectable, non-reference sequences, we prioritize potentially damaging mutations by mining public databases for functional effects. We confirm documented mutations in Jurkat and propose links from detrimental gene variants to observed expression abnormalities in the cell line.    Conclusions  The Jurkat cell line harbors many mutations that are associated with cancer and contribute to Jurkat’s unique characteristics. Genes with damaging mutations in the Jurkat cell line are involved in T-cell receptor signaling ( PTEN ,  INPP5D ,  CTLA4 , and  SYK ), maintenance of genome stability ( TP53 ,  BAX , and  MSH2 ), and O-linked glycosylation ( C1GALT1C1 ). This work ties together decades of molecular experiments and serves as a resource that will streamline both the interpretation of past research and the design of future Jurkat studies.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4718-6) contains supplementary material, which is available to authorized users.

A genome-wide survey of mutations in the Jurkat cell line