http://genome.sph.umich.edu/w/index.php?action=history&feed=atom&title=Outcomes_For_Mapping_A_Paired_End 2026-10-15T15:04:09Z Revision history for this page on the wiki MediaWiki 1.43.1 http://genome.sph.umich.edu/w/index.php?title=Outcomes_For_Mapping_A_Paired_End&diff=505&oldid=prev 2010-02-19T20:52:55Z

<p>Created page with &#039;== Basics == Paired end reads have an expected relative orientation (for example, FR are expected to map to opposite strands of the genome) and distance (for example, 500 bp +/-…&#039;</p> <p><b>New page</b></p><div>== Basics ==<br /> <br /> Paired end reads have an expected relative orientation (for example, FR are expected to map to opposite strands of the genome) and distance (for example, 500 bp +/- 100 bp apart).<br /> <br /> == Possible Mapping Outcomes ==<br /> <br /> === Proper Mapping ===<br /> <br /> Reasonable alignment for the pair, which places both reads in the expected orientation and at the expected separation.<br /> <br /> Most fragments should map like this.<br /> <br /> === Improper Pairs ===<br /> <br /> Sometimes, the reads can be mapped individually, but don&#039;t map with the expected orientation and/or separation. <br /> <br /> Clusters of reads that don&#039;t map as expected can suggested re-arrangements in the DNA sample being sequenced (such as insertions, deletions, inversions and translocations).<br /> <br /> === Only One End Maps ===<br /> <br /> Sometimes, only one end can be matched to genome confidently. The other end might be low in quality, might overlap a sequence that is not present in the reference genome, or might be overlap a sequence re-arrangement such as deletion or insertion.<br /> <br /> Clusters of reads such as this can be used to detect re-arrangements. <br /> <br /> Sometimes the unmapped pair might be placed using a local alignment algorithm that allows for insertions and deletions in the neighborhood of the mapped read.</div>

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