Shear-splink allows semiquantitative analysis of insertional mutations. (A) Southern blot analysis with an MMTV-LTR specific probe shows (in addition to the internal MMTV fragment) three bands representing endogenous MMTV copies in the FVB genome. Clonal MMTV mammary tumor cell lines BB12 and AE6 contain different patterns of somatic MMTV insertions. (B) Overview of total sequence read numbers containing a unique LP for each mixing ratio of BB12 and AE6 DNA. (C) Mixing of BB12 and AE6 DNA does not affect the number of unique LPs for a somatic MMTV insertion that is present in both cell lines. (D,E) Somatic MMTV insertions that are unique for BB12 or AE6 show numbers of unique LPs that correlate with relative clonality of the insertions (R² > 0.86 for five out of six insertions).