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 Mapped52827888.214%
Wrongly Mapped6864711.463%
Not Mapped19330.323%
Total598858100.0%
Read Failure Statistics
Not mapped19330.323%
Missing in mapper output00.0%
Mapped to wrong chromosome409206.833%
Mapped to wrong position277274.63%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.937400
Precision0.885000
Recall0.996400
Timing
Raw Mapping Time66.408s
Effective Mapping Time65.800s
Effective Init Time0.608s
Effective Time MeasureCPU
Mapping Time (Wall)28.540s
Mapping Time (CPU)66.408s
Mapping Time (CPU User)64.316s
Mapping Time (CPU System)2.092s
Init Time (Wall)0.588s
Init Time (CPU)0.608s
Init Time (CPU User)0.168s
Init Time (CPU System)0.440s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)140.064s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.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/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory222044000
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
systime0.488
time16.1863679886
usrtime0.168
working_directory/project/teaser/genometeaser/tests_generated/63224990d2f5aeaa3b674d6cbc4acc8f

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory222208000
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
systime0.44
time0.587563037872
usrtime0.168
working_directory/project/teaser/genometeaser/tests_generated/63224990d2f5aeaa3b674d6cbc4acc8f

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/D_melanogaster.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory236444000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1933 (0.32%) aligned 0 times
485344 (81.04%) aligned exactly 1 time
111581 (18.63%) aligned >1 times
99.68% overall alignment rate
systime2.092
time28.5395169258
usrtime64.316
working_directory/project/teaser/genometeaser/tests_generated/63224990d2f5aeaa3b674d6cbc4acc8f