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 Mapped72266282.928%
Wrongly Mapped10385111.917%
Not Mapped449205.155%
Total871433100.0%
Read Failure Statistics
Not mapped449205.155%
Missing in mapper output00.0%
Mapped to wrong chromosome868859.97%
Mapped to wrong position169591.946%
Mapped to wrong strand70.001%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.906700
Precision0.874400
Recall0.941500
Timing
Raw Mapping Time47.760s
Effective Mapping Time44.932s
Effective Init Time2.828s
Effective Time MeasureCPU
Mapping Time (Wall)24.427s
Mapping Time (CPU)47.760s
Mapping Time (CPU User)44.828s
Mapping Time (CPU System)2.932s
Init Time (Wall)2.897s
Init Time (CPU)2.828s
Init Time (CPU User)0.016s
Init Time (CPU System)2.812s
Additional Information
Mapper Memory Usage2338 MB
Total Test Runtime (Wall)346.136s
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
memory2336228000
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
systime4.812
time203.613792896
usrtime0.012
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698

/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
systime2.812
time2.89740800858
usrtime0.016
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698

/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
memory2338776000
return0
status1
stderr
None
stdout
# reads processed: 871433
# reads with at least one reported alignment: 826513 (94.85%)
# reads that failed to align: 44920 (5.15%)
Reported 826513 alignments to 1 output stream(s)
systime2.932
time24.4269421101
usrtime44.828
working_directory/project/teaser/genometeaser/tests_generated/913dd6b6c8f0bd5901b65d962c7cd698