Detection of virus integration sites in five NGS samplesa.

N/A: not available. –: software did not end within allowable time. ×: software failure. aOnly the samples in Table 1 that harbor virus integration sites are included in this table (HeLa cervical cancer cell line was excluded from this table because a large chromosomal region in 8q24 instead of a precise virus insertion position was provided for this sample [7]). bIt is the test data of ViralFusionSeq [11]. The virus integration sites of this sample were validated but are not publically available. ViralFusionSeq outputs human-virus fusion sequences instead of fusion breakpoints. Its predictions of virus integration sites for the first two samples, 198T and 268T, were taken from its published paper. When running ViralFusionSeq on the sample HCC cell line HKCI-5, we got the intermediate results that indicate a virus integration site around chr16:30408324. Its user manual provides another position, chr7: 98532184- 98532285, for this sample. Both loci were included here for the purpose of comparison.