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 Mapped52785388.143%
Wrongly Mapped6911111.54%
Not Mapped18940.316%
Total598858100.0%
Read Failure Statistics
Not mapped18940.316%
Missing in mapper output00.0%
Mapped to wrong chromosome411766.876%
Mapped to wrong position279354.665%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.937000
Precision0.884200
Recall0.996400
Timing
Raw Mapping Time66.640s
Effective Mapping Time66.048s
Effective Init Time0.592s
Effective Time MeasureCPU
Mapping Time (Wall)28.579s
Mapping Time (CPU)66.640s
Mapping Time (CPU User)64.848s
Mapping Time (CPU System)1.792s
Init Time (Wall)0.579s
Init Time (CPU)0.592s
Init Time (CPU User)0.148s
Init Time (CPU System)0.444s
Additional Information
Mapper Memory Usage238 MB
Total Test Runtime (Wall)152.384s
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
memory224252000
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
time16.1338591576
usrtime0.16
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51

/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
memory222048000
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
systime0.444
time0.579173088074
usrtime0.148
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51

/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
memory238460000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1894 (0.32%) aligned 0 times
485810 (81.12%) aligned exactly 1 time
111154 (18.56%) aligned >1 times
99.68% overall alignment rate
systime1.792
time28.5791580677
usrtime64.848
working_directory/project/teaser/genometeaser/tests_generated/940d34bf07c6143b2e6e8116a29b2b51