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 Mapped28057193.524%
Wrongly Mapped48431.614%
Not Mapped145864.862%
Total300000100.0%
Read Failure Statistics
Not mapped145864.862%
Missing in mapper output00.0%
Mapped to wrong chromosome38791.293%
Mapped to wrong position9640.321%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.966500
Precision0.983000
Recall0.950600
Timing
Raw Mapping Time102.680s
Effective Mapping Time102.608s
Effective Init Time0.072s
Effective Time MeasureCPU
Mapping Time (Wall)45.102s
Mapping Time (CPU)102.680s
Mapping Time (CPU User)98.588s
Mapping Time (CPU System)4.092s
Init Time (Wall)0.489s
Init Time (CPU)0.072s
Init Time (CPU User)0.012s
Init Time (CPU System)0.060s
Additional Information
Mapper Memory Usage234 MB
Total Test Runtime (Wall)95.383s
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: 0.129 sec; CPU: 0.064 sec
systime0.056
time0.156055927277
usrtime0.02
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

/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: 0.367 sec; CPU: 0.064 sec
systime0.06
time0.489130973816
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972

/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
memory234992000
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: 45.050 sec; CPU: 102.648 sec
systime4.092
time45.1020030975
usrtime98.588
working_directory/project/teaser/genometeaser/tests_generated/37932f46d81271bed2cae5ca41c9d972