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 Mapped23898495.594%
Wrongly Mapped95753.83%
Not Mapped14410.576%
Total250000100.0%
Read Failure Statistics
Not mapped14410.576%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position95753.83%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.977500
Precision0.961500
Recall0.994000
Timing
Raw Mapping Time19.668s
Effective Mapping Time19.280s
Effective Init Time0.388s
Effective Time MeasureCPU
Mapping Time (Wall)10.591s
Mapping Time (CPU)19.668s
Mapping Time (CPU User)18.716s
Mapping Time (CPU System)0.952s
Init Time (Wall)0.338s
Init Time (CPU)0.388s
Init Time (CPU User)0.112s
Init Time (CPU System)0.276s
Additional Information
Mapper Memory Usage74 MB
Total Test Runtime (Wall)58.451s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.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/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory64504000
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
systime0.256
time2.30457210541
usrtime0.152
working_directory/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads_base.fastq -S out_bowtie2.sam
memory66548000
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
systime0.276
time0.338403940201
usrtime0.112
working_directory/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/E_coli.fasta_bt -U reads.fastq -S out_bowtie2.sam
memory74564000
return0
status1
stderr
None
stdout
250000 reads; of these:
250000 (100.00%) were unpaired; of these:
1441 (0.58%) aligned 0 times
233734 (93.49%) aligned exactly 1 time
14825 (5.93%) aligned >1 times
99.42% overall alignment rate
systime0.952
time10.5913391113
usrtime18.716
working_directory/project/teaser/genometeaser/tests_generated/4e92df353baa1274023a9524957cd99f