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 Mapped52899588.334%
Wrongly Mapped6797511.351%
Not Mapped18880.315%
Total598858100.0%
Read Failure Statistics
Not mapped18880.315%
Missing in mapper output00.0%
Mapped to wrong chromosome406536.788%
Mapped to wrong position273224.562%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.938100
Precision0.886100
Recall0.996400
Timing
Raw Mapping Time119.888s
Effective Mapping Time117.880s
Effective Init Time2.008s
Effective Time MeasureCPU
Mapping Time (Wall)58.755s
Mapping Time (CPU)119.888s
Mapping Time (CPU User)116.348s
Mapping Time (CPU System)3.540s
Init Time (Wall)2.751s
Init Time (CPU)2.008s
Init Time (CPU User)0.172s
Init Time (CPU System)1.836s
Additional Information
Mapper Memory Usage236 MB
Total Test Runtime (Wall)216.547s
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
memory222044000
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
systime1.028
time22.2986910343
usrtime0.196
working_directory/project/teaser/genometeaser/tests_generated/c474138b0d14daeadd1924f6eed36587

/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
memory220424000
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
systime1.836
time2.75096893311
usrtime0.172
working_directory/project/teaser/genometeaser/tests_generated/c474138b0d14daeadd1924f6eed36587

/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
memory236348000
return0
status1
stderr
None
stdout
598858 reads; of these:
598858 (100.00%) were unpaired; of these:
1888 (0.32%) aligned 0 times
486437 (81.23%) aligned exactly 1 time
110533 (18.46%) aligned >1 times
99.68% overall alignment rate
systime3.54
time58.7551560402
usrtime116.348
working_directory/project/teaser/genometeaser/tests_generated/c474138b0d14daeadd1924f6eed36587