samtools stats typical ranges and explicit definitions

Question

[dec986]

hello,

I am looking for more thorough documentation than what is provided for samtools stats http://www.htslib.org/doc/samtools.html because I have no idea what typical ranges are for lots of these values, specifically the ones that show up with "SN"

For example, what is a good quality score? What is a good range for MQ0? what are typical ranges for error rate? Samtools' "non-primary alignment" isn't defined. I can't find any information on this online.

[Carlo Yague]

Mapping quality = −10 * log10 Pr{mapping position is wrong}, rounded to the nearest integer. Higher quality means higher score. For instance if samtools believed that the pobability that the mapping position is correct is of 90%, then your MQ = -10 * log10(0.1) = 10. If the probabilty is 99%, MQ=20.

Non-primary alignments is generally equivalent to secondary alignments:

A secondary alignment occurs when a given read could align reasonably well to more than one place. One of the possible reported alignments is termed "primary" and the others will be marked as "secondary". – Devon Ryan