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 Mapped3238897.165%
Wrongly Mapped9362.808%
Not Mapped90.027%
Total33333100.0%
Read Failure Statistics
Not mapped90.027%
Missing in mapper output00.0%
Mapped to wrong chromosome00.0%
Mapped to wrong position9362.808%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.985600
Precision0.971900
Recall0.999700
Timing
Raw Mapping Time63.188s
Effective Mapping Time62.780s
Effective Init Time0.408s
Effective Time MeasureCPU
Mapping Time (Wall)19.231s
Mapping Time (CPU)63.188s
Mapping Time (CPU User)62.316s
Mapping Time (CPU System)0.872s
Init Time (Wall)0.342s
Init Time (CPU)0.408s
Init Time (CPU User)0.140s
Init Time (CPU System)0.268s
Additional Information
Mapper Memory Usage117 MB
Total Test Runtime (Wall)43.703s
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
memory64352000
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
systime0.28
time2.24599790573
usrtime0.116
working_directory/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e

/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
memory64348000
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
systime0.268
time0.342274904251
usrtime0.14
working_directory/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e

/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
memory117084000
return0
status1
stderr
None
stdout
33333 reads; of these:
33333 (100.00%) were unpaired; of these:
9 (0.03%) aligned 0 times
31715 (95.15%) aligned exactly 1 time
1609 (4.83%) aligned >1 times
99.97% overall alignment rate
systime0.872
time19.2308390141
usrtime62.316
working_directory/project/teaser/genometeaser/tests_generated/4c21a44c9042d3b44a6729ccaaa2740e