Mapping Quality Thresholds

The plot below shows the percentages of correctly and wrongly mapped reads for all mapping quality thresholds for this mapper. The values at threshold 0 therefore correspond to the unfiltered results.

Basic Statistics
Correctly Mapped28074293.581%
Wrongly Mapped47601.587%
Not Mapped144984.833%
Total300000100.0%
Read Failure Statistics
Not mapped144984.833%
Missing in mapper output00.0%
Mapped to wrong chromosome38841.295%
Mapped to wrong position8760.292%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.966800
Precision0.983300
Recall0.950900
Timing
Raw Mapping Time97.496s
Effective Mapping Time97.448s
Effective Init Time0.048s
Effective Time MeasureCPU
Mapping Time (Wall)39.015s
Mapping Time (CPU)97.496s
Mapping Time (CPU User)93.200s
Mapping Time (CPU System)4.296s
Init Time (Wall)0.118s
Init Time (CPU)0.048s
Init Time (CPU User)0.012s
Init Time (CPU System)0.036s
Additional Information
Mapper Memory Usage235 MB
Total Test Runtime (Wall)73.576s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq -t 4 > out_bwasw.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory48832000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.194 sec; CPU: 0.040 sec
systime0.036
time0.214293956757
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory48832000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 1 sequences/pairs (60 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads_base.fastq
[main] Real time: 0.087 sec; CPU: 0.040 sec
systime0.036
time0.117759943008
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a

/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq -t 4 > out_bwasw.sam
memory235652000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 300000 sequences/pairs (15000000 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Saccharomyces_cerevisiae.fasta reads.fastq
[main] Real time: 38.977 sec; CPU: 97.468 sec
systime4.296
time39.0149459839
usrtime93.2
working_directory/project/teaser/genometeaser/tests_generated/50d3e669ec8fd54ec3ae5364036f143a