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 Mapped52722388.038%
Wrongly Mapped6976311.649%
Not Mapped18720.313%
Total598858100.0%
Read Failure Statistics
Not mapped18720.313%
Missing in mapper output00.0%
Mapped to wrong chromosome417986.98%
Mapped to wrong position279654.67%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.936400
Precision0.883100
Recall0.996500
Timing
Raw Mapping Time73.616s
Effective Mapping Time72.668s
Effective Init Time0.948s
Effective Time MeasureCPU
Mapping Time (Wall)30.804s
Mapping Time (CPU)73.616s
Mapping Time (CPU User)70.580s
Mapping Time (CPU System)3.036s
Init Time (Wall)1.017s
Init Time (CPU)0.948s
Init Time (CPU User)0.100s
Init Time (CPU System)0.848s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)119.515s
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
memory221000000
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
systime1.32
time16.0732040405
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/36c0b9ed4ca2236f8f8f48f19e427ab8

/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
memory221532000
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
systime0.848
time1.01727795601
usrtime0.1
working_directory/project/teaser/genometeaser/tests_generated/36c0b9ed4ca2236f8f8f48f19e427ab8

/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
memory236240000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1872 (0.31%) aligned 0 times
483374 (80.72%) aligned exactly 1 time
113612 (18.97%) aligned >1 times
99.69% overall alignment rate
systime3.036
time30.803850174
usrtime70.58
working_directory/project/teaser/genometeaser/tests_generated/36c0b9ed4ca2236f8f8f48f19e427ab8