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 Mapped38950093.213%
Wrongly Mapped168094.023%
Not Mapped115512.764%
Total417860100.0%
Read Failure Statistics
Not mapped115512.764%
Missing in mapper output00.0%
Mapped to wrong chromosome66961.602%
Mapped to wrong position101132.42%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment6
Secondary Alignments0
F-Measure0.964900
Precision0.958600
Recall0.971200
Timing
Raw Mapping Time145.860s
Effective Mapping Time145.688s
Effective Init Time0.172s
Effective Time MeasureCPU
Mapping Time (Wall)70.610s
Mapping Time (CPU)145.860s
Mapping Time (CPU User)140.228s
Mapping Time (CPU System)5.632s
Init Time (Wall)0.220s
Init Time (CPU)0.172s
Init Time (CPU User)0.012s
Init Time (CPU System)0.160s
Additional Information
Mapper Memory Usage484 MB
Total Test Runtime (Wall)120.082s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/C_elegans.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/C_elegans.fa reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq -t 4 > out_bwasw.sam
memory174864000
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/C_elegans.fa reads_base.fastq
[main] Real time: 0.191 sec; CPU: 0.156 sec
systime0.156
time0.215755939484
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/C_elegans.fa reads_base.fastq -t 4 > out_bwasw.sam
memory174864000
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/C_elegans.fa reads_base.fastq
[main] Real time: 0.188 sec; CPU: 0.156 sec
systime0.16
time0.220364809036
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/C_elegans.fa reads.fastq -t 4 > out_bwasw.sam
memory484832000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 417860 sequences/pairs (25071600 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/C_elegans.fa reads.fastq
[main] Real time: 70.562 sec; CPU: 145.820 sec
systime5.632
time70.6099689007
usrtime140.228
working_directory/project/teaser/genometeaser/tests_generated/0b75acea7debea0665280a94869c22a6