In the sam le you will have the following elds pos

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Unformatted text preview: will randomly pick one posi0on and give it a mapping quality zero. •  Q=25 the edit distance equals mismatches and is greater than zero What to do with low quality scores? •  Find repeat structures in the genome/con0g. •  Determine if there is a problem with your alignment or data (i.e. all the reads mapped with low quality scores). •  Filter them out. Very common to write a perl/ python script to filter out poorly aligned reads. •  Many, many, many other possibili0es. The Alignment Column CIGAR String •  CIGAR string is a compact representa0on of how the read aligned to the reference genome at that exact posi0on. •  More specifically, the CIGAR string is a sequence of of base lengths and the associated opera0on. –  match/mismatch with the reference. –  deleted/inser...
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