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 Mapped74810385.847%
Wrongly Mapped10289011.807%
Not Mapped204402.346%
Total871433100.0%
Read Failure Statistics
Not mapped204402.346%
Missing in mapper output00.0%
Mapped to wrong chromosome859459.862%
Mapped to wrong position169391.944%
Mapped to wrong strand60.001%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.923800
Precision0.879100
Recall0.973400
Timing
Raw Mapping Time188.008s
Effective Mapping Time152.084s
Effective Init Time35.924s
Effective Time MeasureCPU
Mapping Time (Wall)108.244s
Mapping Time (CPU)188.008s
Mapping Time (CPU User)99.540s
Mapping Time (CPU System)88.468s
Init Time (Wall)36.194s
Init Time (CPU)35.924s
Init Time (CPU User)0.108s
Init Time (CPU System)35.816s
Additional Information
Mapper Memory Usage3379 MB
Total Test Runtime (Wall)342.971s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_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/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3359644000
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
systime57.24
time116.833282948
usrtime0.124
working_directory/project/teaser/genometeaser/tests_generated/49efbf792a671892244ba9297cc6202a

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory3359664000
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
systime35.816
time36.1940720081
usrtime0.108
working_directory/project/teaser/genometeaser/tests_generated/49efbf792a671892244ba9297cc6202a

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/H_sapiens.fa_bt -U reads.fastq -S out_bowtie2.sam
memory3379696000
return0
status1
stderr
None
stdout
871433 reads; of these:
871433 (100.00%) were unpaired; of these:
20440 (2.35%) aligned 0 times
632064 (72.53%) aligned exactly 1 time
218929 (25.12%) aligned >1 times
97.65% overall alignment rate
systime88.468
time108.243665934
usrtime99.54
working_directory/project/teaser/genometeaser/tests_generated/49efbf792a671892244ba9297cc6202a