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 Mapped64866982.708%
Wrongly Mapped8281010.559%
Not Mapped528116.734%
Total784290100.0%
Read Failure Statistics
Not mapped528116.734%
Missing in mapper output00.0%
Mapped to wrong chromosome680088.671%
Mapped to wrong position147981.887%
Mapped to wrong strand40.001%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.905400
Precision0.886800
Recall0.924700
Timing
Raw Mapping Time46.596s
Effective Mapping Time45.084s
Effective Init Time1.512s
Effective Time MeasureCPU
Mapping Time (Wall)23.674s
Mapping Time (CPU)46.596s
Mapping Time (CPU User)43.572s
Mapping Time (CPU System)3.024s
Init Time (Wall)1.579s
Init Time (CPU)1.512s
Init Time (CPU User)0.004s
Init Time (CPU System)1.508s
Additional Information
Mapper Memory Usage2338 MB
Total Test Runtime (Wall)128.958s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads.fastq out_bowtie.sam
Errors and Warnings
No problems were encountered.
Subprocess Log

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam
memory2336136000
return0
status1
stderr
None
stdout
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
systime2.44
time2.52341198921
usrtime0.008
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads_base.fastq out_bowtie.sam
memory2336212000
return0
status1
stderr
None
stdout
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
systime1.508
time1.57896900177
usrtime0.004
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f

/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads.fastq out_bowtie.sam

command/project/teaser/genometeaser/software/bowtie --threads 4 -S /project/teaser/genometeaser/references/H_sapiens.fa_bo reads.fastq out_bowtie.sam
memory2338832000
return0
status1
stderr
None
stdout
# reads processed: 784290
# reads with at least one reported alignment: 731479 (93.27%)
# reads that failed to align: 52811 (6.73%)
Reported 731479 alignments to 1 output stream(s)
systime3.024
time23.6744570732
usrtime43.572
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f