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 Mapped29200097.604%
Wrongly Mapped71482.389%
Not Mapped210.007%
Total299169100.0%
Read Failure Statistics
Not mapped210.007%
Missing in mapper output00.0%
Mapped to wrong chromosome26650.891%
Mapped to wrong position44831.498%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.987900
Precision0.976100
Recall0.999900
Timing
Raw Mapping Time55.436s
Effective Mapping Time54.888s
Effective Init Time0.548s
Effective Time MeasureCPU
Mapping Time (Wall)22.150s
Mapping Time (CPU)55.436s
Mapping Time (CPU User)53.876s
Mapping Time (CPU System)1.560s
Init Time (Wall)0.487s
Init Time (CPU)0.548s
Init Time (CPU User)0.132s
Init Time (CPU System)0.416s
Additional Information
Mapper Memory Usage207 MB
Total Test Runtime (Wall)94.901s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_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/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory196292000
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
systime0.496
time13.7064421177
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads_base.fastq -S out_bowtie2.sam
memory202688000
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
systime0.416
time0.48711681366
usrtime0.132
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Arabidopsis_thaliana.fas_bt -U reads.fastq -S out_bowtie2.sam
memory207744000
return0
status1
stderr
None
stdout
299169 reads; of these:
299169 (100.00%) were unpaired; of these:
21 (0.01%) aligned 0 times
252526 (84.41%) aligned exactly 1 time
46622 (15.58%) aligned >1 times
99.99% overall alignment rate
systime1.56
time22.1498100758
usrtime53.876
working_directory/project/teaser/genometeaser/tests_generated/85176433619c96b494ede3b93198c48c