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 Mapped52734988.059%
Wrongly Mapped6962511.626%
Not Mapped18840.315%
Total598858100.0%
Read Failure Statistics
Not mapped18840.315%
Missing in mapper output00.0%
Mapped to wrong chromosome416256.951%
Mapped to wrong position280004.676%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.936500
Precision0.883400
Recall0.996400
Timing
Raw Mapping Time60.592s
Effective Mapping Time60.008s
Effective Init Time0.584s
Effective Time MeasureCPU
Mapping Time (Wall)27.135s
Mapping Time (CPU)60.592s
Mapping Time (CPU User)58.776s
Mapping Time (CPU System)1.816s
Init Time (Wall)0.529s
Init Time (CPU)0.584s
Init Time (CPU User)0.164s
Init Time (CPU System)0.420s
Additional Information
Mapper Memory Usage238 MB
Total Test Runtime (Wall)135.896s
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
memory222272000
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
systime0.432
time0.541156053543
usrtime0.156
working_directory/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0

/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
systime0.42
time0.528678178787
usrtime0.164
working_directory/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0

/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:
1884 (0.31%) aligned 0 times
484789 (80.95%) aligned exactly 1 time
112185 (18.73%) aligned >1 times
99.69% overall alignment rate
systime1.816
time27.1347780228
usrtime58.776
working_directory/project/teaser/genometeaser/tests_generated/58281c12b324089e734fe0553bf2f5c0