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 Mapped14597397.315%
Wrongly Mapped37572.505%
Not Mapped2700.18%
Total150000100.0%
Read Failure Statistics
Not mapped2700.18%
Missing in mapper output00.0%
Mapped to wrong chromosome17631.175%
Mapped to wrong position19941.329%
Mapped to wrong strand00.0%
Advanced Statistics
Missing in comparison alignment0
Secondary Alignments0
F-Measure0.986400
Precision0.974900
Recall0.998200
Timing
Raw Mapping Time20.434s
Effective Mapping Time20.239s
Effective Init Time0.195s
Effective Time MeasureCPU
Mapping Time (Wall)5.741s
Mapping Time (CPU)20.434s
Mapping Time (CPU User)20.081s
Mapping Time (CPU System)0.353s
Init Time (Wall)0.243s
Init Time (CPU)0.195s
Init Time (CPU User)0.063s
Init Time (CPU System)0.132s
Additional Information
Mapper Memory Usage83 MB
Total Test Runtime (Wall)16.972s
Mapper Command Line: 
/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa_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/Schizosaccharomyces_pombe.fa_bt -U reads_base.fastq -S out_bowtie2.sam

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory59724000
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
systime0.132979
time0.591825008392
usrtime0.055991
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa_bt -U reads_base.fastq -S out_bowtie2.sam
memory60548000
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
systime0.131979
time0.242561817169
usrtime0.06299
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157

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

command/project/teaser/genometeaser/software/bowtie2/bowtie2 -p 4 -x /project/teaser/genometeaser/references/Schizosaccharomyces_pombe.fa_bt -U reads.fastq -S out_bowtie2.sam
memory83160000
return0
status1
stderr
None
stdout
150000 reads; of these:
150000 (100.00%) were unpaired; of these:
270 (0.18%) aligned 0 times
142986 (95.32%) aligned exactly 1 time
6744 (4.50%) aligned >1 times
99.82% overall alignment rate
systime0.352946
time5.74083900452
usrtime20.080947
working_directory/project/teaser/genometeaser/tests_generated/78245a202e759eede079b41dad2c7157