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Further information on creating a consensus scaffold map, a second method for anchoring scaffolds, calling sex of the F2s, and fine mapping of recombinant breakpoints are presented in Supplemental Methods in File S8.
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Multiple breakpoints are present in most of the cell lines, revealing these positions may be highly rearranged.
KYSE30 is the cell line with the most complex rearrangements, and array-CGH results have also indicated that much more breakpoints were present in KYSE30 than the other cell lines, which are consistent with M-FISH results.
The breakpoint zone diameters used in the study, and respective minimum inhibitory concentrations (MIC), if available, are presented in Table 1.
The fraction of the reads supporting the mutation (left and right breakpoints averaged) is presented in Additional file 3: Table S1.
A more in-depth comparison between MDL partitioning and related methods of recombination breakpoint detection is presented in the discussion.
A summary of the estimated breakpoints for all autosomes is presented in Table 2.
The CYP2C19 deletion carrier frequency was only marginally higher in the breast cancer cases (31/842, 3.7%) when compared to the controls (17/497, 3.4%), being relatively high in both groups (sequence of the CYP2C19 deletion breakpoints and its surrounding area is presented in Additional file 2: Figure S1).
The "common deletion" involving the 13 nt direct repeat at the breakpoint was present in 25 patients (25/67 = 37%).
Specifically, the function will intersect the R eff = 1 line twice when a worm breakpoint is present in the system and the value of worm intensity occurring at the lower of these two intersections will be the breakpoint (Additional File 1, Figure 1).
The detected SNPs were presented in Additional file 7. A bin map was constructed with 35,128 recombination breakpoints for all lines, in which each line contained an average of 125 breakpoints.
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