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 Mapped57318691.354%
Wrongly Mapped492557.85%
Not Mapped49910.795%
Total627432100.0%
Read Failure Statistics
Not mapped49910.795%
Missing in mapper output00.0%
Mapped to wrong chromosome384566.129%
Mapped to wrong position107981.721%
Mapped to wrong strand10.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.954800
Precision0.920900
Recall0.991400
Timing
Raw Mapping Time120.892s
Effective Mapping Time117.484s
Effective Init Time3.408s
Effective Time MeasureCPU
Mapping Time (Wall)44.042s
Mapping Time (CPU)120.892s
Mapping Time (CPU User)114.780s
Mapping Time (CPU System)6.112s
Init Time (Wall)3.360s
Init Time (CPU)3.408s
Init Time (CPU User)0.124s
Init Time (CPU System)3.284s
Additional Information
Mapper Memory Usage3383 MB
Total Test Runtime (Wall)155.215s
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
memory3361560000
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
systime3.34
time3.40367007256
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb

/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
memory3361500000
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
systime3.284
time3.36003017426
usrtime0.124
working_directory/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb

/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
memory3383024000
return0
status1
stderr
None
stdout
627432 reads; of these:
627432 (100.00%) were unpaired; of these:
4991 (0.80%) aligned 0 times
478661 (76.29%) aligned exactly 1 time
143780 (22.92%) aligned >1 times
99.20% overall alignment rate
systime6.112
time44.0423839092
usrtime114.78
working_directory/project/teaser/genometeaser/tests_generated/0ae17b2547a4a7bf1a0dbd8dcfe180bb