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 Mapped29161097.473%
Wrongly Mapped73532.458%
Not Mapped2060.069%
Total299169100.0%
Read Failure Statistics
Not mapped2060.069%
Missing in mapper output00.0%
Mapped to wrong chromosome27770.928%
Mapped to wrong position45761.53%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment4
Secondary Alignments0
F-Measure0.987200
Precision0.975400
Recall0.999300
Timing
Raw Mapping Time149.952s
Effective Mapping Time149.728s
Effective Init Time0.224s
Effective Time MeasureCPU
Mapping Time (Wall)47.788s
Mapping Time (CPU)149.952s
Mapping Time (CPU User)145.444s
Mapping Time (CPU System)4.508s
Init Time (Wall)0.270s
Init Time (CPU)0.224s
Init Time (CPU User)0.004s
Init Time (CPU System)0.220s
Additional Information
Mapper Memory Usage528 MB
Total Test Runtime (Wall)88.748s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas 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/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam
memory209380000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.233 sec; CPU: 0.208 sec
systime0.216
time0.255666017532
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads_base.fastq -t 4 > out_bwasw.sam
memory209384000
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/Arabidopsis_thaliana.fas reads_base.fastq
[main] Real time: 0.241 sec; CPU: 0.212 sec
systime0.22
time0.2698969841
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq -t 4 > out_bwasw.sam
memory528096000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 299169 sequences/pairs (29916900 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas reads.fastq
[main] Real time: 47.742 sec; CPU: 149.912 sec
systime4.508
time47.7878530025
usrtime145.444
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c