WT mapping alignmentReport oddities.

[KevinLam]

Can someone kindly explain "Reads mapped, not filtered" in plain english?
ABI's documentation is confusing (put mildly)

The 100.0% value reported for the “Reads mapped, not filtered” line should
be interpreted as “Reads mapped, not filtered” comprising 100% of the
category described in its section, not that the category “Reads mapped, not
filtered” comprises 100% of the total reads.


Fun stuff to note.
(reads mapped) - (reads filtered ) != (Reads mapped, not filtered )

samtools flagstat Sample1.filtered.bam
11023236 in total
9020807 mapped (81.83%)
Why would unmapped in the filtered bam be considered filtered sequences?



--------------
ALIGNMENT REPORT
--------------

Counts:
Total reads: 72,150,924 (100.0%)
Reads mapped: 46,888,011 ( 65.0%)
Reads filtered: 11,023,236 ( 15.3%)
-----
Reads mapped, not filtered 37,867,204 (100.0%)
Reads with too many mappings (N >= 10): 4,335,633 ( 11.4%)
Reads with number of mappings in proper range (N < 10): 33,531,571 ( 88.6%)
Reads uniquely aligned (score.clear.zone = 5): 26,128,221 ( 69.0%)
Reads uniquely aligned to junctions 1,514,252 ( 4.0%)
Reads uniquely aligned to known junctions 1,501,926 ( 4.0%)

ABSOLUTE FREQUENCIES
Alignment_Score All_Read_Alignments_(N_=_46888011) Primary_Read_Alignments_(N_=_37867204) Unique_Read_Alignments_(N_=_26128221)