Samtools difference between Mapped and Unmapped read
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10 weeks ago
Sean • 0

Hello,

I am wondering what the difference is between a mapped and unmapped read in samtools.

I am extremely new to this whole process, just trying to learn my way through so if you could "dumb" it down or try and explain it in a simpler way that would be helpful. Thank you

unmapped samtools mapped • 254 views
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A mapped read is a read for which the aligner could find a fitting spot in the genome (an alignment). For an unmapped read, no suitable alignment was found.

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While it is not light reading it may help to take a look at the SAM file format specification. Mandatory fields in alignments are in section 1.4. Field number three refers to "Reference Name".

An unmapped segment (read) without coordinate has a ‘*’ at this field.

Otherwise there will be the name of reference segment the read aligns to e.g. chr1.

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