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 Mapped7420.124%
Wrongly Mapped58542597.757%
Not Mapped126912.119%
Total598858100.0%
Read Failure Statistics
Not mapped126912.119%
Missing in mapper output00.0%
Mapped to wrong chromosome48118780.351%
Mapped to wrong position10423817.406%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.002500
Precision0.001300
Recall0.055200
Timing
Raw Mapping Time63.730s
Effective Mapping Time63.488s
Effective Init Time0.242s
Effective Time MeasureCPU
Mapping Time (Wall)17.942s
Mapping Time (CPU)63.730s
Mapping Time (CPU User)62.794s
Mapping Time (CPU System)0.936s
Init Time (Wall)0.293s
Init Time (CPU)0.242s
Init Time (CPU User)0.065s
Init Time (CPU System)0.177s
Additional Information
Mapper Memory Usage234 MB
Total Test Runtime (Wall)52.655s
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
memory193312000
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
systime0.131979
time0.214674949646
usrtime0.045993
working_directory/project/teaser/genometeaser/tests_generated/3d3edd8a6a451905ff28f5063d73cc4e

/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
memory208376000
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
systime0.176973
time0.292856931686
usrtime0.06499
working_directory/project/teaser/genometeaser/tests_generated/3d3edd8a6a451905ff28f5063d73cc4e

/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
memory234268000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
12691 (2.12%) aligned 0 times
477852 (79.79%) aligned exactly 1 time
108315 (18.09%) aligned >1 times
97.88% overall alignment rate
systime0.935857
time17.9424200058
usrtime62.794453
working_directory/project/teaser/genometeaser/tests_generated/3d3edd8a6a451905ff28f5063d73cc4e