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 Mapped68471484.91%
Wrongly Mapped9325611.564%
Not Mapped284343.526%
Total806404100.0%
Read Failure Statistics
Not mapped284343.526%
Missing in mapper output00.0%
Mapped to wrong chromosome558606.927%
Mapped to wrong position373954.637%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment67
Secondary Alignments0
F-Measure0.918400
Precision0.880100
Recall0.960100
Timing
Raw Mapping Time422.092s
Effective Mapping Time414.580s
Effective Init Time7.512s
Effective Time MeasureCPU
Mapping Time (Wall)154.749s
Mapping Time (CPU)422.092s
Mapping Time (CPU User)398.896s
Mapping Time (CPU System)23.196s
Init Time (Wall)7.602s
Init Time (CPU)7.512s
Init Time (CPU User)0.156s
Init Time (CPU System)7.356s
Additional Information
Mapper Memory Usage8760 MB
Total Test Runtime (Wall)268.048s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.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/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8272068000
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/M_musculus.fasta reads_base.fastq
[main] Real time: 7.520 sec; CPU: 7.440 sec
systime7.296
time7.54180717468
usrtime0.16
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory8271940000
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/M_musculus.fasta reads_base.fastq
[main] Real time: 7.572 sec; CPU: 7.492 sec
systime7.356
time7.60152482986
usrtime0.156
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq -t 4 > out_bwasw.sam
memory8760044000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 666668 sequences/pairs (40000080 bp) ...
[bsw2_aln] read 139736 sequences/pairs (8384160 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/M_musculus.fasta reads.fastq
[main] Real time: 154.692 sec; CPU: 422.076 sec
systime23.196
time154.748978853
usrtime398.896
working_directory/project/teaser/genometeaser/tests_generated/023be73dabd493f04945e37217bf7c31