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samtools stats typical ranges and explicit definitions

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.

samtools rna-seq
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written by dec986 dec986

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

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written by Carlo Yague Carlo Yague

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