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 Mapped74828585.868%
Wrongly Mapped10270211.785%
Not Mapped204462.346%
Total871433100.0%
Read Failure Statistics
Not mapped204462.346%
Missing in mapper output00.0%
Mapped to wrong chromosome852299.78%
Mapped to wrong position174692.005%
Mapped to wrong strand40.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.924000
Precision0.879300
Recall0.973400
Timing
Raw Mapping Time131.844s
Effective Mapping Time97.784s
Effective Init Time34.060s
Effective Time MeasureCPU
Mapping Time (Wall)55.690s
Mapping Time (CPU)131.844s
Mapping Time (CPU User)92.768s
Mapping Time (CPU System)39.076s
Init Time (Wall)34.099s
Init Time (CPU)34.060s
Init Time (CPU User)0.072s
Init Time (CPU System)33.988s
Additional Information
Mapper Memory Usage3379 MB
Total Test Runtime (Wall)182.587s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads.fastq -S out_bowtie2.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3359420000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime37.216
time38.7931001186
usrtime0.088
working_directory/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3359028000
return0
status1
stderr
None
stdout
1 reads; of these:
1 (100.00%) were unpaired; of these:
1 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
systime33.988
time34.0987241268
usrtime0.072
working_directory/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads.fastq -S out_bowtie2.sam
memory3379496000
return0
status1
stderr
None
stdout
871433 reads; of these:
871433 (100.00%) were unpaired; of these:
20446 (2.35%) aligned 0 times
631912 (72.51%) aligned exactly 1 time
219075 (25.14%) aligned >1 times
97.65% overall alignment rate
systime39.076
time55.6898458004
usrtime92.768
working_directory/project/teaser/genometeaser/tests_generated/dbe9c301671e3f72d169833f77afc52d