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Genomic coordinates of the paired-end based SV calls from SVDetect were compared with the fragmented alignments of the assembled contigs and breakpoints were determined for SV calls supported by the assembly.
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Recombination breakpoints were determined by checking the positions where genotypes change.
Recombination breakpoints were determined by the junction of two different genotypes.
Consensus daughter sequences and breakpoints were determined whenever possible.
Breakpoints were determined molecularly by genomic PCR and sequencing.
These new breakpoints were determined using the pharmacokinetic-pharmacodynamic properties of antimicrobial agents and minimal inhibitory concentration (MIC) distributions for relevant organisms [ 2, 3].
Breakpoints were determined by splitting reads with at least one member of a pair mapping to one of the two loci for an event, and remapping.
In both of these studies, precise breakpoints and unambiguous copy numbers were determined for each analyzed sample.
20 bp sequences spanning the pairs of breakpoints were compared, aligning the breakpoints with each other, and the extent of 100% sequence identity flanking/spanning the breakpoints was determined.
A P-value for any specified breakpoint was determined by the Fisher's exact test (two-tailed).
Although the method used for the first breakpoint could not work for the second breakpoint, the second breakpoint was determined using the V-slope method with two straight-line approximations, which was developed to detect an anaerobic threshold (Schneider et al., 1993).
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