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 Mapped32127689.586%
Wrongly Mapped339959.479%
Not Mapped33520.935%
Total358623100.0%
Read Failure Statistics
Not mapped33520.935%
Missing in mapper output00.0%
Mapped to wrong chromosome183625.12%
Mapped to wrong position156334.359%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment30
Secondary Alignments0
F-Measure0.945100
Precision0.904300
Recall0.989700
Timing
Raw Mapping Time425.120s
Effective Mapping Time372.096s
Effective Init Time53.024s
Effective Time MeasureCPU
Mapping Time (Wall)190.430s
Mapping Time (CPU)425.120s
Mapping Time (CPU User)314.748s
Mapping Time (CPU System)110.372s
Init Time (Wall)53.883s
Init Time (CPU)53.024s
Init Time (CPU User)0.012s
Init Time (CPU System)53.012s
Additional Information
Mapper Memory Usage4943 MB
Total Test Runtime (Wall)343.525s
Mapper Command Line: 
/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus_cutf.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/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwasw.sam

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory4661464000
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/M_musculus_cutf.fasta reads_base.fastq
[main] Real time: 55.606 sec; CPU: 54.732 sec
systime54.74
time55.6332368851
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads_base.fastq -t 4 > out_bwasw.sam
memory4661552000
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/M_musculus_cutf.fasta reads_base.fastq
[main] Real time: 53.849 sec; CPU: 53.012 sec
systime53.012
time53.8833429813
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

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

command/project/teaser/genometeaser/software/bwa bwasw /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq -t 4 > out_bwasw.sam
memory4943700000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 358623 sequences/pairs (27255348 bp) ...
[main] Version: 0.7.16a-r1181
[main] CMD: /project/teaser/genometeaser/software/bwa bwasw -t 4 /project/teaser/genometeaser/references/M_musculus_cutf.fasta reads.fastq
[main] Real time: 190.360 sec; CPU: 425.088 sec
systime110.372
time190.430212021
usrtime314.748
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9