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 Mapped52761788.104%
Wrongly Mapped6932711.577%
Not Mapped19140.32%
Total598858100.0%
Read Failure Statistics
Not mapped19140.32%
Missing in mapper output00.0%
Mapped to wrong chromosome416316.952%
Mapped to wrong position276964.625%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.936800
Precision0.883900
Recall0.996400
Timing
Raw Mapping Time59.551s
Effective Mapping Time59.314s
Effective Init Time0.237s
Effective Time MeasureCPU
Mapping Time (Wall)16.713s
Mapping Time (CPU)59.551s
Mapping Time (CPU User)58.648s
Mapping Time (CPU System)0.903s
Init Time (Wall)0.261s
Init Time (CPU)0.237s
Init Time (CPU User)0.057s
Init Time (CPU System)0.180s
Additional Information
Mapper Memory Usage233 MB
Total Test Runtime (Wall)50.542s
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
memory208116000
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
systime0.315951
time2.62800312042
usrtime0.073988
working_directory/project/teaser/genometeaser/tests_generated/465464d523f5a7eb9d2d48753a117599

/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
memory213824000
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
systime0.179972
time0.261252880096
usrtime0.056991
working_directory/project/teaser/genometeaser/tests_generated/465464d523f5a7eb9d2d48753a117599

/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
memory233952000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1914 (0.32%) aligned 0 times
484706 (80.94%) aligned exactly 1 time
112238 (18.74%) aligned >1 times
99.68% overall alignment rate
systime0.902862
time16.7127120495
usrtime58.648084
working_directory/project/teaser/genometeaser/tests_generated/465464d523f5a7eb9d2d48753a117599