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 Mapped13155987.706%
Wrongly Mapped48693.246%
Not Mapped135729.048%
Total150000100.0%
Read Failure Statistics
Not mapped135729.048%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position48693.246%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.934500
Precision0.964300
Recall0.906500
Timing
Raw Mapping Time30.696s
Effective Mapping Time30.324s
Effective Init Time0.372s
Effective Time MeasureCPU
Mapping Time (Wall)17.379s
Mapping Time (CPU)30.696s
Mapping Time (CPU User)29.000s
Mapping Time (CPU System)1.696s
Init Time (Wall)0.378s
Init Time (CPU)0.372s
Init Time (CPU User)0.096s
Init Time (CPU System)0.276s
Additional Information
Mapper Memory Usage76 MB
Total Test Runtime (Wall)56.497s
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
memory62396000
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
systime0.224
time0.680209875107
usrtime0.072
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

/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
memory52884000
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
time0.378086805344
usrtime0.096
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558

/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
memory76540000
return0
status1
stderr
None
stdout
150000 reads; of these:
150000 (100.00%) were unpaired; of these:
13572 (9.05%) aligned 0 times
128937 (85.96%) aligned exactly 1 time
7491 (4.99%) aligned >1 times
90.95% overall alignment rate
systime1.696
time17.3786580563
usrtime29.0
working_directory/project/teaser/genometeaser/tests_generated/a588fafacb71f50b55e5a5739e179558