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Old 06-11-2017, 12:39 PM   #14
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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"perfect" means every base in the read matched the reference (no mismatches, indels, or Ns). "semiperfect" is similar but it allows Ns in the reference.

The "num reads" column in "mapped" row indicates the number of reads that were mapped.

Don't worry about the high error rate. That just indicates that 63.8% of your reads had at least one error (mismatching base, indel, etc). The more important number is the % of bases, which is only 0.46%, so the reads have roughly 99.5% identity to the reference.
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