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 Mapped65495875.159%
Wrongly Mapped9598611.015%
Not Mapped12048913.827%
Total871433100.0%
Read Failure Statistics
Not mapped12048913.827%
Missing in mapper output00.0%
Mapped to wrong chromosome811609.313%
Mapped to wrong position148201.701%
Mapped to wrong strand60.001%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.858200
Precision0.872200
Recall0.844600
Timing
Raw Mapping Time179.204s
Effective Mapping Time175.812s
Effective Init Time3.392s
Effective Time MeasureCPU
Mapping Time (Wall)81.769s
Mapping Time (CPU)179.204s
Mapping Time (CPU User)164.088s
Mapping Time (CPU System)15.116s
Init Time (Wall)15.465s
Init Time (CPU)3.392s
Init Time (CPU User)0.080s
Init Time (CPU System)3.312s
Additional Information
Mapper Memory Usage5917 MB
Total Test Runtime (Wall)215.718s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.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/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5366504000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 10.158 sec; CPU: 4.480 sec
systime4.428
time11.2115371227
usrtime0.076
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads_base.fastq -t 4 > out_bwasw.sam
memory5365028000
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/H_sapiens.fa reads_base.fastq
[main] Real time: 13.872 sec; CPU: 3.376 sec
systime3.312
time15.4649829865
usrtime0.08
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq -t 4 > out_bwasw.sam
memory5917392000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 871433 sequences/pairs (31371588 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/H_sapiens.fa reads.fastq
[main] Real time: 80.242 sec; CPU: 179.180 sec
systime15.116
time81.7688279152
usrtime164.088
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698