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 Mapped50220396.049%
Wrongly Mapped202373.87%
Not Mapped4200.08%
Total522860100.0%
Read Failure Statistics
Not mapped4200.08%
Missing in mapper output00.0%
Mapped to wrong chromosome131832.521%
Mapped to wrong position70521.349%
Mapped to wrong strand20.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.979800
Precision0.961300
Recall0.999200
Timing
Raw Mapping Time193.852s
Effective Mapping Time190.124s
Effective Init Time3.728s
Effective Time MeasureCPU
Mapping Time (Wall)55.410s
Mapping Time (CPU)193.852s
Mapping Time (CPU User)184.572s
Mapping Time (CPU System)9.280s
Init Time (Wall)3.722s
Init Time (CPU)3.728s
Init Time (CPU User)0.092s
Init Time (CPU System)3.636s
Additional Information
Mapper Memory Usage3400 MB
Total Test Runtime (Wall)440.274s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.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
memory3359372000
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
systime4.516
time289.446233034
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/24f21f076cb23e5eaf20f9023e376370

/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
memory3359096000
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
systime3.636
time3.72203302383
usrtime0.092
working_directory/project/teaser/genometeaser/tests_generated/24f21f076cb23e5eaf20f9023e376370

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -1 reads1.fastq -2 reads2.fastq -S out_bowtie2.sam
memory3400840000
return0
status1
stderr
None
stdout
261430 reads; of these:
261430 (100.00%) were paired; of these:
29144 (11.15%) aligned concordantly 0 times
197812 (75.67%) aligned concordantly exactly 1 time
34474 (13.19%) aligned concordantly >1 times
----
29144 pairs aligned concordantly 0 times; of these:
22611 (77.58%) aligned discordantly 1 time
----
6533 pairs aligned 0 times concordantly or discordantly; of these:
13066 mates make up the pairs; of these:
420 (3.21%) aligned 0 times
1203 (9.21%) aligned exactly 1 time
11443 (87.58%) aligned >1 times
99.92% overall alignment rate
systime9.28
time55.410337925
usrtime184.572
working_directory/project/teaser/genometeaser/tests_generated/24f21f076cb23e5eaf20f9023e376370