I'm using BBMap (mapPacBio) to map cDNA reads from a nanopore sequencer. I got the results below, and I'm a little confused as to how I've got a 75% mapped rate, but NA match rate, and 86%+ for all errors. Also <0.0065 perfect/semiperfect sites and <0.4% N.

I might be misunderstanding what these statistics mean, but is this maybe because long reads are more prone to have an error within them, and match rate = perfect match?

Any help would be wonderful!

Thanks!

(I also used usemodulo due to memory limitations on the computer I have access to at home during lockdown. A fuller explanation of what this is would also be greatly appreciated!)

chris@chris-Virtual-Machine:~/data$ bbmap/mapPacBio.sh ref=genomic.fna in=bc01.fastq outm=bbout/C1_R1.sam outu=bbout/C1_R1_unmapped.sam -Xmx19g -da usemodulo=t qin=33 maxlen=5000
java -da -Xmx19g -cp /home/chris/data/bbmap/current/ align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 ref=genomic.fna in=bc01.fastq outm=bbout/C1_R1.sam outu=bbout/C1_R1_unmapped.sam -Xmx19g -da usemodulo=t qin=33 maxlen=5000
Executing align2.BBMapPacBio [build=1, overwrite=true, minratio=0.40, fastareadlen=6000, ambiguous=best, minscaf=100, startpad=10000, stoppad=10000, midpad=6000, ref=genomic.fna, in=bc01.fastq, outm=bbout/C1_R1.sam, outu=bbout/C1_R1_unmapped.sam, -Xmx19g, -da, usemodulo=t, qin=33, maxlen=5000]
Version 38.84

Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.400
Retaining first best site only for ambiguous mappings.
NOTE:   Ignoring reference file because it already appears to have been processed.
NOTE:   If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Set genome to 1

Loaded Reference:       41.380 seconds.
Loading index for chunk 1-7, build 1
Generated Index:        3.107 seconds.
Analyzed Index:         2.173 seconds.
Started output stream:  0.273 seconds.
Started output stream:  0.006 seconds.
Cleared Memory:         0.138 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 12 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11

   ------------------   Results   ------------------

Genome:                 1
Key Length:             12
Max Indel:              100
Minimum Score Ratio:    0.4
Mapping Mode:           normal
Reads Used:             130792  (246593288 bases)

Mapping:                13642.747 seconds.
Reads/sec:              9.59
kBases/sec:             18.08


Read 1 data:            pct reads       num reads       pct bases          num bases

mapped:                  74.7026%           97705        78.9886%          194780668
unambiguous:             35.9250%           46987        45.4884%          112171292
ambiguous:               38.7776%           50718        33.5003%           82609376
low-Q discards:           0.1820%             238         0.0147%              36209

perfect best site:        0.0054%               7         0.0001%                303
semiperfect site:         0.0054%               7         0.0001%                303

Match Rate:                   NA               NA        77.7629%          166855321
Error Rate:              86.0866%           97698        22.1700%           47570066
Sub Rate:                86.0699%           97679         5.9545%           12776573
Del Rate:                85.9985%           97598         9.2225%           19788575
Ins Rate:                85.9818%           97579         6.9930%           15004918
N Rate:                   0.3622%             411         0.0670%             143856

Total time:             13690.052 seconds.