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 Mapped145747975.308%
Wrongly Mapped39339920.327%
Not Mapped844924.366%
Total1935370100.0%
Read Failure Statistics
Not mapped844924.366%
Missing in mapper output00.0%
Mapped to wrong chromosome28746814.853%
Mapped to wrong position1059255.473%
Mapped to wrong strand60.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.859100
Precision0.787500
Recall0.945200
Timing
Raw Mapping Time533.240s
Effective Mapping Time471.256s
Effective Init Time61.984s
Effective Time MeasureCPU
Mapping Time (Wall)161.813s
Mapping Time (CPU)533.240s
Mapping Time (CPU User)453.924s
Mapping Time (CPU System)79.316s
Init Time (Wall)62.499s
Init Time (CPU)61.984s
Init Time (CPU User)0.120s
Init Time (CPU System)61.864s
Additional Information
Mapper Memory Usage3104 MB
Total Test Runtime (Wall)771.694s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_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/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3088088000
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
systime33.668
time269.9990592
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory3088240000
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
systime61.864
time62.4994881153
usrtime0.12
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/M_musculus.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory3104652000
return0
status1
stderr
None
stdout
1935370 reads; of these:
1935370 (100.00%) were unpaired; of these:
84492 (4.37%) aligned 0 times
1288791 (66.59%) aligned exactly 1 time
562087 (29.04%) aligned >1 times
95.63% overall alignment rate
systime79.316
time161.813212872
usrtime453.924
working_directory/project/teaser/genometeaser/tests_generated/43bdd5cc22aa7c6d1994fe8ebc8d72d4