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 Mapped75201586.296%
Wrongly Mapped10217511.725%
Not Mapped172431.979%
Total871433100.0%
Read Failure Statistics
Not mapped172431.979%
Missing in mapper output00.0%
Mapped to wrong chromosome852929.788%
Mapped to wrong position168761.937%
Mapped to wrong strand70.001%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.926400
Precision0.880400
Recall0.977600
Timing
Raw Mapping Time87.880s
Effective Mapping Time83.712s
Effective Init Time4.168s
Effective Time MeasureCPU
Mapping Time (Wall)38.097s
Mapping Time (CPU)87.880s
Mapping Time (CPU User)82.876s
Mapping Time (CPU System)5.004s
Init Time (Wall)4.141s
Init Time (CPU)4.168s
Init Time (CPU User)0.104s
Init Time (CPU System)4.064s
Additional Information
Mapper Memory Usage3379 MB
Total Test Runtime (Wall)429.410s
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
memory3361720000
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
systime6.92
time289.432571888
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698

/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
memory3358324000
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
systime4.064
time4.14101719856
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698

/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
memory3379264000
return0
status1
stderr
None
stdout
871433 reads; of these:
871433 (100.00%) were unpaired; of these:
17243 (1.98%) aligned 0 times
633122 (72.65%) aligned exactly 1 time
221068 (25.37%) aligned >1 times
98.02% overall alignment rate
systime5.004
time38.0972599983
usrtime82.876
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698