Fig. 1

Illustration of HiNT. a Hi-C read pairs are classified into normal pairs (left panel), unambiguous chimeric pairs (middle panel), and ambiguous chimeric pairs (right panel). Hi-C unambiguous chimeric pairs are the product of Hi-C ligations in which one read crosses the ligation junction and thus maps to both locus A and locus B, while the other normal read maps only to locus B. Hi-C ambiguous chimeric pairs are often caused by structural variations, with one read mapping to both locus A and locus C, while the other read maps to locus B. b Copy number information is reflected in the Hi-C 1D coverage profile after Hi-C biases are removed by normalizing the K562 Hi-C contact matrix with the GM12878 Hi-C contact matrix. The copy number profile (log2 ratios) estimated from WGS data is shown in the bottom row for comparison. c Comparison of the Hi-C contact matrix between chr9 and chr19 in samples with and without translocations. The distribution of normalized contact frequencies is higher in the sample with translocation (purple dots) than in the sample without (cyan dots). Contact frequencies were calculated in 1-Mb bins in chr9 and chr19