Samtools difference between Mapped and Unmapped read

Question

[Sean]

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

[WouterDeCoster]

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.

[GenoMax]

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.