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Unfortunately, we did not obtained the complete sequence, because the insert size of clone P3DP22F02 was only 578 base pairs.
Because the insert size usually exceeds the length of a single read, read-pairs may match up unique regions surrounding repeats that are longer than the read length.
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The choice of 200 bp was because the insert sizes of the data we analyzed were mostly between 150 and 200; we also used 100 bp as a threshold and similar patterns of results were observed (data not shown).
The validity at 10 kb of these scaffolds is low because SOPRA's estimate of the insert size is not accurate.
Slight differences in mapq scores are expected because their calculation takes into account the insert size statistics, which are calculated on sample windows on the input stream of sequences.
Consider M read-pair libraries, which are sorted in the order of increasing insert sizes and the associated decision rules Extend i(P) for 1 ≤ i ≤ M. We process the libraries in this order because our analysis revealed that the smaller is the insert size of a library (and its variation), the more reliable is the decision rule for this individual library.
The insert size was approximately 200 bp.
The insert size range is 35-290 kb.
The insert size of the library was approximately 200 bp.
The insert size of the library was ~306 bp.
The insert size distribution is shown in Figure 1.
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