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 Mapped14577597.183%
Wrongly Mapped37552.503%
Not Mapped4700.313%
Total150000100.0%
Read Failure Statistics
Not mapped4700.313%
Missing in mapper output00.0%
Mapped to wrong chromosome20021.335%
Mapped to wrong position17531.169%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment5
Secondary Alignments0
F-Measure0.985700
Precision0.974900
Recall0.996800
Timing
Raw Mapping Time76.362s
Effective Mapping Time76.341s
Effective Init Time0.021s
Effective Time MeasureCPU
Mapping Time (Wall)21.714s
Mapping Time (CPU)76.362s
Mapping Time (CPU User)75.940s
Mapping Time (CPU System)0.422s
Init Time (Wall)0.055s
Init Time (CPU)0.021s
Init Time (CPU User)0.000s
Init Time (CPU System)0.021s
Additional Information
Mapper Memory Usage155 MB
Total Test Runtime (Wall)31.065s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa 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/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwasw.sam
memory22664000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq
[main] Real time: 0.050 sec; CPU: 0.015 sec
systime0.014997
time0.054710149765
usrtime0.001999
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq -t 4 > out_bwasw.sam
memory22656000
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: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads_base.fastq
[main] Real time: 0.034 sec; CPU: 0.019 sec
systime0.020996
time0.054661989212
usrtime0.0
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq -t 4 > out_bwasw.sam
memory155720000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 150000 sequences/pairs (15000000 bp) ...
[main] Version: 0.7.12-r1039
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa reads.fastq
[main] Real time: 21.705 sec; CPU: 76.356 sec
systime0.421935
time21.7140848637
usrtime75.940455
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157