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 Mapped24952191.55%
Wrongly Mapped226198.299%
Not Mapped4130.152%
Total272553100.0%
Read Failure Statistics
Not mapped4130.152%
Missing in mapper output00.0%
Mapped to wrong chromosome111624.095%
Mapped to wrong position114574.204%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment26
Secondary Alignments0
F-Measure0.955900
Precision0.916900
Recall0.998300
Timing
Raw Mapping Time339.700s
Effective Mapping Time335.208s
Effective Init Time4.492s
Effective Time MeasureCPU
Mapping Time (Wall)98.186s
Mapping Time (CPU)339.700s
Mapping Time (CPU User)329.000s
Mapping Time (CPU System)10.700s
Init Time (Wall)4.595s
Init Time (CPU)4.492s
Init Time (CPU User)0.056s
Init Time (CPU System)4.436s
Additional Information
Mapper Memory Usage4958 MB
Total Test Runtime (Wall)148.188s
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
memory4663060000
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: 4.872 sec; CPU: 4.804 sec
systime4.74
time4.8995411396
usrtime0.072
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

/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
memory4661372000
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: 4.551 sec; CPU: 4.476 sec
systime4.436
time4.59524178505
usrtime0.056
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d

/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
memory4958540000
return0
status1
stderr
None
stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[bsw2_aln] read 272553 sequences/pairs (27255300 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: 98.053 sec; CPU: 339.664 sec
systime10.7
time98.1861679554
usrtime329.0
working_directory/project/teaser/genometeaser/tests_generated/ef84d4ed82d0fef31ff0765d0f19324d