To evaluate QTFPred’s performance in predicting TF binding signals at base resolution, we benchmarked it against BPNet and FCNsignal [34] (Supplementary Method S4) using 49 ChIP-seq datasets from three human cell lines (Supplementary Table S2): cervical carcinoma cell line from human cervix (HeLa-S3: 12 TFs), chronic myelogenous leukemia cell line from human blood (K562: 17 TFs), and B-lymphoblastoid cell line from human blood (GM12878: 20 TFs). Here, TF is linked to chronic myelogenous leukemia, BCR-ABL1 positive.