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 Mapped9313093.13%
Wrongly Mapped35553.555%
Not Mapped33153.315%
Total100000100.0%
Read Failure Statistics
Not mapped33153.315%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position35553.555%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.964400
Precision0.963200
Recall0.965600
Timing
Raw Mapping Time38.784s
Effective Mapping Time37.988s
Effective Init Time0.796s
Effective Time MeasureCPU
Mapping Time (Wall)19.303s
Mapping Time (CPU)38.784s
Mapping Time (CPU User)36.396s
Mapping Time (CPU System)2.388s
Init Time (Wall)0.847s
Init Time (CPU)0.796s
Init Time (CPU User)0.152s
Init Time (CPU System)0.644s
Additional Information
Mapper Memory Usage78 MB
Total Test Runtime (Wall)57.621s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_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/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory61972000
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
systime0.42
time2.66356110573
usrtime0.14
working_directory/project/teaser/genometeaser/tests_generated/30952ba36f06792420203f74b83db277

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory61180000
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
systime0.644
time0.846672058105
usrtime0.152
working_directory/project/teaser/genometeaser/tests_generated/30952ba36f06792420203f74b83db277

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory78632000
return0
status1
stderr
None
stdout
100000 reads; of these:
100000 (100.00%) were unpaired; of these:
3315 (3.31%) aligned 0 times
90902 (90.90%) aligned exactly 1 time
5783 (5.78%) aligned >1 times
96.69% overall alignment rate
systime2.388
time19.3028569221
usrtime36.396
working_directory/project/teaser/genometeaser/tests_generated/30952ba36f06792420203f74b83db277