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 Mapped68606387.476%
Wrongly Mapped8240110.506%
Not Mapped158262.018%
Total784290100.0%
Read Failure Statistics
Not mapped158262.018%
Missing in mapper output00.0%
Mapped to wrong chromosome671348.56%
Mapped to wrong position152641.946%
Mapped to wrong strand30.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.933200
Precision0.892800
Recall0.977500
Timing
Raw Mapping Time97.412s
Effective Mapping Time93.780s
Effective Init Time3.632s
Effective Time MeasureCPU
Mapping Time (Wall)39.666s
Mapping Time (CPU)97.412s
Mapping Time (CPU User)91.956s
Mapping Time (CPU System)5.456s
Init Time (Wall)3.635s
Init Time (CPU)3.632s
Init Time (CPU User)0.088s
Init Time (CPU System)3.544s
Additional Information
Mapper Memory Usage3382 MB
Total Test Runtime (Wall)121.238s
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
memory3359516000
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
systime3.588
time3.67796301842
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f

/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
memory3361496000
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
systime3.544
time3.6350581646
usrtime0.088
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f

/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
memory3382336000
return0
status1
stderr
None
stdout
784290 reads; of these:
784290 (100.00%) were unpaired; of these:
15826 (2.02%) aligned 0 times
577102 (73.58%) aligned exactly 1 time
191362 (24.40%) aligned >1 times
97.98% overall alignment rate
systime5.456
time39.6664290428
usrtime91.956
working_directory/project/teaser/genometeaser/tests_generated/550e44394139b4f9ff4d8f5d1ede8a8f