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 Mapped71021088.071%
Wrongly Mapped9316411.553%
Not Mapped30300.376%
Total806404100.0%
Read Failure Statistics
Not mapped30300.376%
Missing in mapper output00.0%
Mapped to wrong chromosome553236.86%
Mapped to wrong position378414.693%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.936600
Precision0.884000
Recall0.995800
Timing
Raw Mapping Time663.480s
Effective Mapping Time564.588s
Effective Init Time98.892s
Effective Time MeasureCPU
Mapping Time (Wall)230.682s
Mapping Time (CPU)663.480s
Mapping Time (CPU User)539.772s
Mapping Time (CPU System)123.708s
Init Time (Wall)100.933s
Init Time (CPU)98.892s
Init Time (CPU User)0.092s
Init Time (CPU System)98.800s
Additional Information
Mapper Memory Usage3154 MB
Total Test Runtime (Wall)755.778s
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
memory3086952000
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
systime168.448
time266.923410892
usrtime0.1
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7

/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
memory3087672000
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
systime98.8
time100.932780981
usrtime0.092
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7

/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
memory3154752000
return0
status1
stderr
None
stdout
806404 reads; of these:
806404 (100.00%) were unpaired; of these:
3030 (0.38%) aligned 0 times
613370 (76.06%) aligned exactly 1 time
190004 (23.56%) aligned >1 times
99.62% overall alignment rate
systime123.708
time230.681970119
usrtime539.772
working_directory/project/teaser/genometeaser/tests_generated/a720be7d510db33409606fe9fee515f7