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 Mapped32426390.419%
Wrongly Mapped338189.43%
Not Mapped5420.151%
Total358623100.0%
Read Failure Statistics
Not mapped5420.151%
Missing in mapper output00.0%
Mapped to wrong chromosome179985.019%
Mapped to wrong position158204.411%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.949700
Precision0.905600
Recall0.998300
Timing
Raw Mapping Time278.952s
Effective Mapping Time242.872s
Effective Init Time36.080s
Effective Time MeasureCPU
Mapping Time (Wall)101.975s
Mapping Time (CPU)278.952s
Mapping Time (CPU User)216.824s
Mapping Time (CPU System)62.128s
Init Time (Wall)36.643s
Init Time (CPU)36.080s
Init Time (CPU User)0.136s
Init Time (CPU System)35.944s
Additional Information
Mapper Memory Usage3148 MB
Total Test Runtime (Wall)469.069s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.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/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3075076000
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
systime28.416
time265.167840958
usrtime0.104
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3075092000
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
systime35.944
time36.6431419849
usrtime0.136
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9

/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus_cutf.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory3148500000
return0
status1
stderr
None
stdout
358623 reads; of these:
358623 (100.00%) were unpaired; of these:
542 (0.15%) aligned 0 times
281254 (78.43%) aligned exactly 1 time
76827 (21.42%) aligned >1 times
99.85% overall alignment rate
systime62.128
time101.975328922
usrtime216.824
working_directory/project/teaser/genometeaser/tests_generated/9616eba5217c671aa1e17d118aefe3c9